Query 022837
Match_columns 291
No_of_seqs 298 out of 1535
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 06:30:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022837.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022837hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2191 RNA-binding protein NO 100.0 3.6E-40 7.7E-45 287.5 24.6 268 4-290 7-281 (402)
2 KOG1676 K-homology type RNA bi 100.0 6.6E-36 1.4E-40 279.3 20.1 215 31-289 135-354 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 5.8E-37 1.3E-41 274.7 10.6 245 30-289 194-447 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 2.3E-32 5E-37 232.7 18.4 241 33-290 46-352 (390)
5 KOG1676 K-homology type RNA bi 100.0 3.4E-32 7.4E-37 254.4 16.2 214 33-289 52-266 (600)
6 KOG2190 PolyC-binding proteins 100.0 1.3E-30 2.9E-35 246.5 23.3 241 33-291 41-294 (485)
7 KOG2193 IGF-II mRNA-binding pr 100.0 5.7E-30 1.2E-34 229.9 9.1 213 29-290 274-530 (584)
8 KOG2190 PolyC-binding proteins 99.9 2.4E-23 5.3E-28 197.2 14.4 201 34-291 137-376 (485)
9 KOG2192 PolyC-binding hnRNP-K 99.9 1.8E-21 3.9E-26 166.3 12.9 160 30-194 118-384 (390)
10 KOG2191 RNA-binding protein NO 99.8 8.3E-21 1.8E-25 166.5 11.8 132 120-289 37-168 (402)
11 TIGR03665 arCOG04150 arCOG0415 99.8 6.6E-19 1.4E-23 146.8 11.4 139 39-196 2-153 (172)
12 PRK13763 putative RNA-processi 99.8 7.8E-18 1.7E-22 141.3 13.1 142 35-196 3-159 (180)
13 cd02396 PCBP_like_KH K homolog 99.6 8.3E-15 1.8E-19 102.6 7.6 64 36-101 1-64 (65)
14 cd02396 PCBP_like_KH K homolog 99.6 1.2E-14 2.5E-19 101.9 7.4 65 123-189 1-65 (65)
15 KOG2279 Kinase anchor protein 99.5 2.8E-14 6E-19 133.2 8.1 241 29-289 62-332 (608)
16 TIGR03665 arCOG04150 arCOG0415 99.4 1.1E-13 2.4E-18 115.4 3.3 111 126-290 2-126 (172)
17 cd02394 vigilin_like_KH K homo 99.4 4.8E-13 1E-17 92.7 5.5 61 124-189 2-62 (62)
18 PRK13763 putative RNA-processi 99.4 3.7E-13 7.9E-18 113.1 5.4 124 122-290 3-132 (180)
19 PF00013 KH_1: KH domain syndr 99.4 4E-13 8.6E-18 92.5 4.4 60 123-188 1-60 (60)
20 PF00013 KH_1: KH domain syndr 99.4 7.4E-13 1.6E-17 91.1 5.2 60 36-101 1-60 (60)
21 cd02393 PNPase_KH Polynucleoti 99.4 2.7E-12 5.9E-17 88.5 7.5 58 122-188 2-60 (61)
22 cd02394 vigilin_like_KH K homo 99.3 1.8E-12 3.9E-17 89.8 5.8 61 37-102 2-62 (62)
23 cd00105 KH-I K homology RNA-bi 99.3 5.9E-12 1.3E-16 87.5 8.0 62 124-188 2-63 (64)
24 cd00105 KH-I K homology RNA-bi 99.3 9.9E-12 2.1E-16 86.4 8.0 62 37-101 2-63 (64)
25 cd02393 PNPase_KH Polynucleoti 99.3 1.6E-11 3.4E-16 84.7 7.7 58 35-101 2-60 (61)
26 PF13014 KH_3: KH domain 99.1 8.5E-11 1.9E-15 75.2 5.5 43 132-176 1-43 (43)
27 PF13014 KH_3: KH domain 99.1 1.2E-10 2.7E-15 74.5 5.6 43 45-89 1-43 (43)
28 COG1094 Predicted RNA-binding 99.1 1.9E-09 4E-14 89.8 12.8 146 33-197 6-167 (194)
29 smart00322 KH K homology RNA-b 99.1 7.1E-10 1.5E-14 77.3 8.9 67 122-193 3-69 (69)
30 smart00322 KH K homology RNA-b 99.0 1.8E-09 3.8E-14 75.2 9.2 67 34-105 2-68 (69)
31 KOG2208 Vigilin [Lipid transpo 98.8 2.4E-08 5.2E-13 100.5 9.3 201 32-290 198-458 (753)
32 KOG2113 Predicted RNA binding 98.8 1.3E-08 2.8E-13 89.7 6.4 140 33-185 24-173 (394)
33 cd02395 SF1_like-KH Splicing f 98.8 3.3E-08 7.2E-13 77.3 8.0 67 130-196 14-97 (120)
34 KOG2208 Vigilin [Lipid transpo 98.6 6.6E-08 1.4E-12 97.3 8.1 146 31-195 343-489 (753)
35 PRK08406 transcription elongat 98.6 8.8E-08 1.9E-12 77.1 7.0 103 36-158 33-135 (140)
36 cd02395 SF1_like-KH Splicing f 98.6 2.9E-07 6.3E-12 72.0 8.0 63 44-106 15-94 (120)
37 TIGR02696 pppGpp_PNP guanosine 98.5 8.6E-07 1.9E-11 87.9 11.0 91 94-194 551-642 (719)
38 KOG2279 Kinase anchor protein 98.4 1.1E-07 2.4E-12 89.6 2.9 113 119-290 65-177 (608)
39 TIGR03591 polynuc_phos polyrib 98.2 4.4E-06 9.6E-11 83.8 9.4 91 95-194 524-615 (684)
40 TIGR01952 nusA_arch NusA famil 98.2 5.3E-06 1.2E-10 66.6 7.0 103 36-158 34-136 (141)
41 KOG0119 Splicing factor 1/bran 98.1 3.6E-05 7.8E-10 72.1 11.3 75 121-195 137-231 (554)
42 PLN00207 polyribonucleotide nu 97.9 2.1E-05 4.5E-10 80.0 7.5 91 95-194 658-750 (891)
43 KOG2113 Predicted RNA binding 97.9 1.4E-05 3.1E-10 70.7 5.0 126 120-287 24-149 (394)
44 COG1185 Pnp Polyribonucleotide 97.9 4.4E-05 9.6E-10 74.6 7.8 102 84-194 506-616 (692)
45 KOG0119 Splicing factor 1/bran 97.8 9.7E-05 2.1E-09 69.3 8.8 74 34-107 137-230 (554)
46 COG0195 NusA Transcription elo 97.7 9.2E-05 2E-09 62.4 6.5 103 36-159 77-179 (190)
47 PRK08406 transcription elongat 97.7 5.6E-05 1.2E-09 60.9 4.9 104 122-289 32-135 (140)
48 KOG1588 RNA-binding protein Sa 97.7 0.00052 1.1E-08 59.9 10.9 79 119-197 89-194 (259)
49 TIGR02696 pppGpp_PNP guanosine 97.7 0.00017 3.8E-09 71.9 8.9 66 32-106 575-641 (719)
50 PRK11824 polynucleotide phosph 97.6 0.0001 2.2E-09 74.2 6.4 91 95-194 527-618 (693)
51 KOG0336 ATP-dependent RNA heli 97.6 0.00011 2.3E-09 68.1 5.4 67 30-102 42-108 (629)
52 KOG0336 ATP-dependent RNA heli 97.6 0.00021 4.5E-09 66.2 7.2 74 119-198 44-117 (629)
53 TIGR03591 polynuc_phos polyrib 97.5 0.00024 5.2E-09 71.5 6.8 64 33-105 549-613 (684)
54 PRK00106 hypothetical protein; 97.4 0.001 2.2E-08 64.7 9.8 67 120-194 223-291 (535)
55 KOG2814 Transcription coactiva 97.4 0.00028 6.1E-09 63.3 5.4 71 34-108 56-126 (345)
56 TIGR03319 YmdA_YtgF conserved 97.4 0.00097 2.1E-08 64.9 9.5 67 120-194 202-270 (514)
57 KOG1588 RNA-binding protein Sa 97.4 0.0013 2.9E-08 57.4 9.3 45 29-73 86-136 (259)
58 cd02134 NusA_KH NusA_K homolog 97.4 0.00037 8.1E-09 47.8 4.7 37 34-70 24-60 (61)
59 PRK12704 phosphodiesterase; Pr 97.3 0.0011 2.4E-08 64.7 9.5 65 121-193 209-275 (520)
60 COG1094 Predicted RNA-binding 97.3 0.00064 1.4E-08 57.0 6.3 53 45-107 112-164 (194)
61 PF14611 SLS: Mitochondrial in 97.2 0.028 6.1E-07 48.3 15.7 131 38-197 29-168 (210)
62 TIGR01953 NusA transcription t 97.1 0.0011 2.4E-08 61.1 6.5 95 44-159 243-338 (341)
63 PRK12328 nusA transcription el 97.1 0.0011 2.4E-08 61.4 6.4 95 44-160 251-346 (374)
64 PRK12327 nusA transcription el 97.1 0.00099 2.2E-08 61.8 6.1 96 44-160 245-341 (362)
65 KOG2814 Transcription coactiva 97.1 0.00077 1.7E-08 60.6 4.7 72 121-196 56-127 (345)
66 cd02134 NusA_KH NusA_K homolog 97.0 0.0011 2.5E-08 45.4 4.5 36 122-157 25-60 (61)
67 PRK00468 hypothetical protein; 97.0 0.00077 1.7E-08 48.2 3.6 35 31-65 26-60 (75)
68 PRK04163 exosome complex RNA-b 96.9 0.0021 4.5E-08 56.4 6.0 65 123-196 146-211 (235)
69 PRK02821 hypothetical protein; 96.9 0.0013 2.8E-08 47.2 3.6 36 31-66 27-62 (77)
70 PRK12329 nusA transcription el 96.9 0.0015 3.3E-08 61.5 5.0 95 44-159 277-372 (449)
71 COG5176 MSL5 Splicing factor ( 96.8 0.0023 4.9E-08 53.9 5.3 41 119-159 145-191 (269)
72 PLN00207 polyribonucleotide nu 96.7 0.0022 4.8E-08 65.6 5.4 66 32-106 682-749 (891)
73 COG1837 Predicted RNA-binding 96.7 0.002 4.3E-08 45.9 3.6 34 32-65 27-60 (76)
74 PRK09202 nusA transcription el 96.6 0.0021 4.6E-08 61.7 4.2 94 45-160 246-340 (470)
75 PRK12705 hypothetical protein; 96.6 0.0053 1.2E-07 59.4 6.8 65 121-193 197-263 (508)
76 COG1185 Pnp Polyribonucleotide 96.6 0.0037 8E-08 61.5 5.4 62 35-105 552-614 (692)
77 KOG1067 Predicted RNA-binding 96.5 0.0069 1.5E-07 58.2 7.0 93 94-196 569-662 (760)
78 PRK01064 hypothetical protein; 96.5 0.0036 7.7E-08 45.1 3.8 34 32-65 27-60 (78)
79 PRK04163 exosome complex RNA-b 96.4 0.0086 1.9E-07 52.5 6.6 62 37-108 147-209 (235)
80 TIGR01952 nusA_arch NusA famil 96.4 0.0038 8.1E-08 50.2 3.8 103 123-289 34-136 (141)
81 COG5176 MSL5 Splicing factor ( 96.3 0.011 2.3E-07 49.9 6.2 40 34-73 147-192 (269)
82 PRK02821 hypothetical protein; 96.3 0.0071 1.5E-07 43.4 4.5 35 119-153 28-62 (77)
83 PRK00468 hypothetical protein; 96.3 0.0049 1.1E-07 44.1 3.6 33 119-151 27-59 (75)
84 COG1837 Predicted RNA-binding 95.9 0.0099 2.1E-07 42.4 3.5 33 119-151 27-59 (76)
85 PRK12704 phosphodiesterase; Pr 95.6 0.032 6.9E-07 54.6 7.0 49 33-89 208-257 (520)
86 PRK11824 polynucleotide phosph 95.5 0.015 3.1E-07 58.9 4.4 63 34-105 553-616 (693)
87 PRK01064 hypothetical protein; 95.5 0.019 4.1E-07 41.3 3.7 33 119-151 27-59 (78)
88 PRK00106 hypothetical protein; 95.5 0.046 1E-06 53.4 7.5 49 33-89 223-272 (535)
89 TIGR03319 YmdA_YtgF conserved 95.5 0.043 9.3E-07 53.6 7.3 49 33-89 202-251 (514)
90 PF13083 KH_4: KH domain; PDB: 95.0 0.011 2.3E-07 41.9 1.2 37 32-68 26-62 (73)
91 KOG4369 RTK signaling protein 94.5 0.036 7.8E-07 57.5 3.7 71 122-194 1340-1410(2131)
92 PF14611 SLS: Mitochondrial in 94.4 0.45 9.7E-06 40.8 10.1 66 122-195 26-91 (210)
93 cd02409 KH-II KH-II (K homolo 94.4 0.079 1.7E-06 36.2 4.3 35 34-68 24-58 (68)
94 cd02410 archeal_CPSF_KH The ar 94.1 0.17 3.8E-06 40.6 6.2 95 49-160 20-114 (145)
95 PF13184 KH_5: NusA-like KH do 93.8 0.051 1.1E-06 38.2 2.4 37 37-73 5-47 (69)
96 COG1855 ATPase (PilT family) [ 93.7 0.077 1.7E-06 50.4 4.0 67 94-161 459-525 (604)
97 PF13083 KH_4: KH domain; PDB: 93.5 0.037 7.9E-07 39.2 1.3 35 119-153 26-60 (73)
98 KOG3273 Predicted RNA-binding 93.4 0.034 7.4E-07 46.7 1.1 56 43-108 177-232 (252)
99 cd02409 KH-II KH-II (K homolo 93.1 0.19 4.2E-06 34.2 4.4 34 122-155 25-58 (68)
100 KOG3273 Predicted RNA-binding 93.1 0.063 1.4E-06 45.1 2.2 150 35-197 74-234 (252)
101 COG1097 RRP4 RNA-binding prote 93.1 0.21 4.5E-06 43.5 5.4 55 39-102 150-205 (239)
102 KOG2874 rRNA processing protei 92.9 0.2 4.3E-06 44.3 5.1 51 134-194 161-211 (356)
103 KOG4369 RTK signaling protein 92.9 0.087 1.9E-06 54.8 3.2 69 32-102 1337-1405(2131)
104 cd02414 jag_KH jag_K homology 92.8 0.13 2.7E-06 36.9 3.2 35 36-70 25-59 (77)
105 PRK13764 ATPase; Provisional 92.6 0.14 3.1E-06 50.8 4.3 66 95-161 455-520 (602)
106 COG1782 Predicted metal-depend 92.4 0.21 4.6E-06 47.9 5.0 97 47-160 41-137 (637)
107 PF13184 KH_5: NusA-like KH do 92.0 0.12 2.6E-06 36.3 2.2 37 123-159 4-46 (69)
108 PF07650 KH_2: KH domain syndr 92.0 0.086 1.9E-06 37.7 1.5 35 35-69 25-59 (78)
109 cd02414 jag_KH jag_K homology 92.0 0.21 4.5E-06 35.7 3.4 34 122-155 24-57 (77)
110 PRK12705 hypothetical protein; 91.8 0.28 6E-06 47.8 5.1 40 34-73 197-237 (508)
111 COG0195 NusA Transcription elo 90.6 0.26 5.6E-06 41.7 3.2 37 36-72 143-179 (190)
112 COG1855 ATPase (PilT family) [ 90.6 0.2 4.3E-06 47.7 2.7 39 36-74 487-525 (604)
113 PF07650 KH_2: KH domain syndr 90.6 0.11 2.4E-06 37.1 0.9 35 122-156 25-59 (78)
114 COG1097 RRP4 RNA-binding prote 90.6 0.83 1.8E-05 39.8 6.3 59 124-191 148-207 (239)
115 KOG2874 rRNA processing protei 90.3 0.51 1.1E-05 41.8 4.8 51 47-107 161-211 (356)
116 PRK12328 nusA transcription el 90.0 0.46 9.9E-06 44.3 4.6 40 35-74 308-347 (374)
117 KOG1067 Predicted RNA-binding 89.8 0.55 1.2E-05 45.7 5.0 99 29-159 591-690 (760)
118 PRK06418 transcription elongat 89.8 0.51 1.1E-05 39.0 4.3 36 37-73 63-98 (166)
119 TIGR03675 arCOG00543 arCOG0054 89.7 0.58 1.3E-05 47.0 5.4 97 47-160 35-131 (630)
120 TIGR01953 NusA transcription t 89.4 0.45 9.8E-06 44.0 4.1 38 35-72 301-338 (341)
121 cd02413 40S_S3_KH K homology R 89.1 0.51 1.1E-05 34.2 3.3 36 36-71 31-66 (81)
122 COG5166 Uncharacterized conser 89.1 0.48 1.1E-05 45.4 4.0 126 48-194 393-524 (657)
123 PRK13764 ATPase; Provisional 89.0 0.34 7.4E-06 48.2 3.1 41 35-75 481-521 (602)
124 cd02413 40S_S3_KH K homology R 87.5 0.75 1.6E-05 33.3 3.4 36 122-157 30-65 (81)
125 PRK12327 nusA transcription el 86.5 0.82 1.8E-05 42.7 3.9 40 34-73 302-341 (362)
126 PRK06418 transcription elongat 86.2 1.1 2.4E-05 37.0 4.1 37 122-159 61-97 (166)
127 PRK09202 nusA transcription el 86.1 0.66 1.4E-05 44.8 3.1 39 35-73 302-340 (470)
128 cd02412 30S_S3_KH K homology R 85.2 0.88 1.9E-05 34.9 2.9 31 37-67 63-93 (109)
129 TIGR00436 era GTP-binding prot 84.7 2.5 5.4E-05 37.6 6.1 30 121-150 220-250 (270)
130 PRK12329 nusA transcription el 84.2 0.99 2.1E-05 42.9 3.3 38 35-72 335-372 (449)
131 PRK15494 era GTPase Era; Provi 84.2 2.6 5.6E-05 39.0 6.1 29 122-150 273-302 (339)
132 cd02411 archeal_30S_S3_KH K ho 84.1 1.2 2.7E-05 32.3 3.2 29 37-65 40-68 (85)
133 cd02410 archeal_CPSF_KH The ar 82.1 1.9 4.1E-05 34.7 3.7 36 38-73 79-114 (145)
134 cd02411 archeal_30S_S3_KH K ho 81.6 1.8 3.8E-05 31.5 3.2 29 123-151 39-67 (85)
135 cd02412 30S_S3_KH K homology R 81.6 1.4 3.1E-05 33.7 2.8 30 123-152 62-91 (109)
136 COG1159 Era GTPase [General fu 80.9 4.5 9.8E-05 36.5 6.0 30 121-150 228-258 (298)
137 KOG1423 Ras-like GTPase ERA [C 80.4 3.4 7.3E-05 37.7 5.0 34 119-152 325-359 (379)
138 COG0092 RpsC Ribosomal protein 80.0 1.7 3.8E-05 37.7 3.0 32 34-65 50-81 (233)
139 PRK03818 putative transporter; 79.3 21 0.00046 35.4 10.8 136 36-188 206-359 (552)
140 COG1847 Jag Predicted RNA-bind 76.0 4.6 0.0001 34.5 4.4 69 120-194 89-158 (208)
141 COG0092 RpsC Ribosomal protein 75.7 2.7 5.9E-05 36.5 3.0 30 121-150 50-79 (233)
142 PRK00089 era GTPase Era; Revie 74.8 7.8 0.00017 34.7 5.9 29 122-150 226-255 (292)
143 TIGR00436 era GTP-binding prot 73.3 4.6 9.9E-05 35.9 4.0 30 35-64 221-251 (270)
144 COG5166 Uncharacterized conser 71.7 15 0.00032 35.7 7.0 103 35-183 449-555 (657)
145 TIGR03675 arCOG00543 arCOG0054 69.9 8 0.00017 39.0 5.2 37 37-73 95-131 (630)
146 COG1782 Predicted metal-depend 66.9 11 0.00023 36.7 5.0 36 37-72 101-136 (637)
147 PRK15494 era GTPase Era; Provi 66.2 7.8 0.00017 35.8 4.0 29 35-63 273-302 (339)
148 PF02749 QRPTase_N: Quinolinat 66.1 19 0.00042 26.2 5.3 54 140-193 32-85 (88)
149 PRK00089 era GTPase Era; Revie 65.7 8.1 0.00018 34.6 4.0 29 35-63 226-255 (292)
150 COG1159 Era GTPase [General fu 65.0 9 0.00019 34.7 4.0 29 35-63 229-258 (298)
151 COG1847 Jag Predicted RNA-bind 64.8 4 8.6E-05 34.9 1.6 36 35-70 91-126 (208)
152 TIGR03802 Asp_Ala_antiprt aspa 63.3 83 0.0018 31.3 10.8 140 35-191 218-379 (562)
153 COG1702 PhoH Phosphate starvat 61.2 19 0.00042 33.3 5.4 53 127-189 20-72 (348)
154 PRK04191 rps3p 30S ribosomal p 60.8 9.5 0.00021 32.7 3.3 31 37-67 42-72 (207)
155 TIGR01008 rpsC_E_A ribosomal p 60.4 10 0.00022 32.3 3.3 31 36-66 39-69 (195)
156 CHL00048 rps3 ribosomal protei 59.7 10 0.00022 32.7 3.3 31 36-66 67-97 (214)
157 PTZ00084 40S ribosomal protein 57.6 11 0.00025 32.6 3.2 32 37-68 46-77 (220)
158 TIGR01008 rpsC_E_A ribosomal p 57.3 12 0.00027 31.8 3.3 30 122-151 38-67 (195)
159 PRK04191 rps3p 30S ribosomal p 56.5 13 0.00027 32.0 3.3 30 123-152 41-70 (207)
160 CHL00048 rps3 ribosomal protei 55.2 14 0.00029 32.0 3.3 30 122-151 66-95 (214)
161 PTZ00084 40S ribosomal protein 53.5 14 0.00031 32.0 3.2 30 122-151 44-73 (220)
162 cd01568 QPRTase_NadC Quinolina 51.0 1.8E+02 0.0039 25.9 10.4 61 132-194 37-98 (269)
163 COG1702 PhoH Phosphate starvat 50.5 50 0.0011 30.6 6.3 53 40-102 20-72 (348)
164 KOG1423 Ras-like GTPase ERA [C 48.2 20 0.00043 32.9 3.3 32 34-65 327-359 (379)
165 cd07055 BMC_like_2 Bacterial M 46.5 59 0.0013 22.1 4.6 36 155-191 25-60 (61)
166 TIGR01009 rpsC_bact ribosomal 43.9 25 0.00053 30.3 3.1 29 37-65 64-92 (211)
167 PF10369 ALS_ss_C: Small subun 43.5 74 0.0016 22.4 5.1 42 142-190 17-58 (75)
168 cd01572 QPRTase Quinolinate ph 43.2 2.4E+02 0.0052 25.1 10.7 55 140-194 43-99 (268)
169 PF09869 DUF2096: Uncharacteri 43.2 87 0.0019 25.9 6.0 55 122-192 113-167 (169)
170 TIGR01009 rpsC_bact ribosomal 41.6 28 0.0006 30.0 3.1 29 123-151 63-91 (211)
171 PF02749 QRPTase_N: Quinolinat 39.7 78 0.0017 22.9 4.9 70 33-106 16-85 (88)
172 PRK15468 carboxysome structura 39.2 52 0.0011 25.1 3.8 47 146-199 57-104 (111)
173 TIGR01334 modD putative molybd 38.2 3E+02 0.0065 24.7 10.6 54 140-193 47-100 (277)
174 cd00652 TBP_TLF TATA box bindi 36.4 2.5E+02 0.0054 23.3 9.6 101 85-194 58-174 (174)
175 PRK06106 nicotinate-nucleotide 35.2 3.1E+02 0.0067 24.7 8.9 53 142-194 57-111 (281)
176 PRK08072 nicotinate-nucleotide 32.7 2.2E+02 0.0047 25.6 7.5 73 122-194 23-105 (277)
177 PRK05848 nicotinate-nucleotide 32.5 1.8E+02 0.0039 26.1 6.9 54 141-194 46-99 (273)
178 PRK00310 rpsC 30S ribosomal pr 32.5 44 0.00096 29.2 3.0 29 37-65 64-92 (232)
179 cd01573 modD_like ModD; Quinol 31.8 3.7E+02 0.0081 23.9 10.4 52 142-193 45-96 (272)
180 COG4010 Uncharacterized protei 30.7 1.9E+02 0.0042 23.3 5.9 44 142-194 126-169 (170)
181 PF00472 RF-1: RF-1 domain; I 29.2 1.1E+02 0.0024 23.4 4.4 48 138-195 23-73 (113)
182 PRK00310 rpsC 30S ribosomal pr 28.8 54 0.0012 28.7 2.9 30 122-151 62-91 (232)
183 TIGR00078 nadC nicotinate-nucl 27.5 2.4E+02 0.0052 25.1 6.9 53 142-194 43-95 (265)
184 PRK08385 nicotinate-nucleotide 26.8 4.7E+02 0.01 23.5 10.6 53 142-194 47-99 (278)
185 cd07046 BMC_PduU-EutS 1,2-prop 26.0 1.2E+02 0.0027 23.2 4.1 29 171-199 75-103 (110)
186 PF00936 BMC: BMC domain; Int 24.0 1.3E+02 0.0029 21.0 3.7 28 168-195 38-65 (75)
187 PF09383 NIL: NIL domain; Int 23.7 1.4E+02 0.0031 20.6 3.8 51 141-191 16-69 (76)
188 PRK07428 nicotinate-nucleotide 23.6 5.5E+02 0.012 23.2 10.6 53 141-193 58-112 (288)
189 PF09869 DUF2096: Uncharacteri 23.0 2.6E+02 0.0057 23.1 5.6 52 35-102 113-164 (169)
190 COG2101 SPT15 TATA-box binding 22.7 2.5E+02 0.0055 23.5 5.5 106 85-194 64-181 (185)
191 CHL00100 ilvH acetohydroxyacid 22.5 4.5E+02 0.0098 21.8 10.0 44 140-190 97-140 (174)
192 PF03958 Secretin_N: Bacterial 21.1 2.7E+02 0.0057 19.2 4.9 24 168-191 53-76 (82)
193 cd06169 BMC Bacterial Micro-Co 21.1 2.2E+02 0.0047 19.0 4.2 25 167-191 37-61 (62)
194 COG0490 Putative regulatory, l 21.0 94 0.002 25.6 2.7 62 123-189 89-158 (162)
195 cd07049 BMC_EutL_repeat1 ethan 20.8 2.4E+02 0.0052 21.4 4.6 48 148-195 46-100 (103)
196 PRK06096 molybdenum transport 20.8 6.3E+02 0.014 22.8 10.5 53 141-193 49-101 (284)
197 PRK15405 ethanolamine utilizat 20.4 5.7E+02 0.012 22.1 10.0 133 58-194 52-209 (217)
No 1
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=3.6e-40 Score=287.50 Aligned_cols=268 Identities=28% Similarity=0.429 Sum_probs=217.9
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCCCCCCCCCc-EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCc
Q 022837 4 NESSYVPSPDVHGKRSTAPVKSLSSDPTEKP-TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTD 82 (291)
Q Consensus 4 ~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~e 82 (291)
.++...-++.++.++++.+....+.+..++. +++|||||+..+|.||||+|++|.+||++|||+|++++..|++|+++|
T Consensus 7 ~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTe 86 (402)
T KOG2191|consen 7 IDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTE 86 (402)
T ss_pred ccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccc
Confidence 4555555667777777766666666665555 999999999999999999999999999999999999999999999999
Q ss_pred eEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCC------CCceEEEEEecCCccceeeccCChhHHHHHHhccceEE
Q 022837 83 RIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDV------GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK 156 (291)
Q Consensus 83 r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~------~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~ 156 (291)
|+|.|+|+.+++....+.|.|+|++..+..+...+. +....++++||+..+|.||||+|.+||.|++++||+|+
T Consensus 87 Rvcli~Gt~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iq 166 (402)
T KOG2191|consen 87 RVCLIQGTVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQ 166 (402)
T ss_pred eEEEEeccHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceE
Confidence 999999999999999999999999986654321211 22245999999999999999999999999999999999
Q ss_pred EecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCC
Q 022837 157 ISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTA 236 (291)
Q Consensus 157 i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~ 236 (291)
|++.++...+..+|+|++.|++++..+|..+|+++|.|||++..++|.+|.|... |..-..| .+
T Consensus 167 isPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsG--------pvaNsnP--------tG 230 (402)
T KOG2191|consen 167 ISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSG--------PVANSNP--------TG 230 (402)
T ss_pred ecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccC--------cccccCC--------CC
Confidence 9986665667789999999999999999999999999999999999977665421 1111111 01
Q ss_pred CCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceEEeec
Q 022837 237 AHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNE 290 (291)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~ 290 (291)
.+|+.. .+..+...+.++.+|+.++|..-|. |+.++-.+...+|+.|.+.+
T Consensus 231 spya~~-~~~~~astas~~sva~~~iG~a~ga--G~~~~a~l~~~~G~l~~itq 281 (402)
T KOG2191|consen 231 SPYAYQ-AHVLPASTASTISVAAGLIGGANGA--GGAFGAALSGFTGALIAITQ 281 (402)
T ss_pred CCCCCC-Cccccccchhhcccccccccccccc--ccccceeeecccccceeecc
Confidence 111111 1224445568889999999999999 99999999999999887754
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=6.6e-36 Score=279.30 Aligned_cols=215 Identities=27% Similarity=0.335 Sum_probs=177.1
Q ss_pred CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc
Q 022837 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH 110 (291)
Q Consensus 31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~ 110 (291)
....++.+|+||.+.+|+||||+|++||+|++++||++.+..++....+ ..+.+.|+|.++.|+.|+.++.+.|.++..
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 3678999999999999999999999999999999999999987654333 678999999999999999999999986522
Q ss_pred ccc-----ccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHH
Q 022837 111 AED-----QADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRAL 185 (291)
Q Consensus 111 ~~~-----~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~ 185 (291)
... .........+.++.||...||.||||+|++||+|+.+||++|+|.++++ +.+.||.+.|.|++++|++|.
T Consensus 214 ~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~--p~speR~~~IiG~~d~ie~Aa 291 (600)
T KOG1676|consen 214 EVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD--PSSPERPAQIIGTVDQIEHAA 291 (600)
T ss_pred CCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC--CCCccceeeeecCHHHHHHHH
Confidence 110 1122234458999999999999999999999999999999999999765 367899999999999999999
Q ss_pred HHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCccee
Q 022837 186 ELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGML 265 (291)
Q Consensus 186 ~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~i 265 (291)
++|.++|++....... +| ..|.|. .....+|.||++++|.|
T Consensus 292 ~lI~eii~~~~~~~~~--------~~----~~G~P~---------------------------~~~~fy~~VPa~KcGLv 332 (600)
T KOG1676|consen 292 ELINEIIAEAEAGAGG--------GM----GGGAPG---------------------------LVAQFYMKVPADKCGLV 332 (600)
T ss_pred HHHHHHHHHHhccCCC--------Cc----CCCCcc---------------------------ceeeEEEeccccccccc
Confidence 9999999985432100 00 001110 00158999999999999
Q ss_pred EEeecCccceehccccccceEEee
Q 022837 266 LIILIAQPIICHFSLSIYEEIRLN 289 (291)
Q Consensus 266 IG~~~gg~~ik~~~~~tga~i~~~ 289 (291)
||| ||++||+|.+++||.+.+.
T Consensus 333 IGr--GGEtIK~in~qSGA~~el~ 354 (600)
T KOG1676|consen 333 IGR--GGETIKQINQQSGARCELS 354 (600)
T ss_pred cCC--CccchhhhcccCCcccccc
Confidence 999 9999999999999999874
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=5.8e-37 Score=274.72 Aligned_cols=245 Identities=23% Similarity=0.321 Sum_probs=189.9
Q ss_pred CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhh
Q 022837 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL 109 (291)
Q Consensus 30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~ 109 (291)
.....+++|+|||..++|.||||.|.|||.|.+.|.|+|+|.+..+ .|..|+.++|-|+++...+|+++|++.|.++.
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA 271 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTSKACKMILEIMQKEA 271 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchHHHHHHHHHHHHHhh
Confidence 3456789999999999999999999999999999999999998765 47889999999999999999999999999884
Q ss_pred ccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837 110 HAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (291)
Q Consensus 110 ~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~ 189 (291)
... +...++.++++.++++||+||||.|.+||+|+.+||++|.|++-.+...-..||+++++|+.++|..|..+|+
T Consensus 272 ~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eIm 347 (584)
T KOG2193|consen 272 VDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIM 347 (584)
T ss_pred hcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHH
Confidence 332 2235688999999999999999999999999999999999998444333346999999999999999999999
Q ss_pred HHHhcCcccC-CCCC-CCccCCCcccC------CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCeEEEeecCC
Q 022837 190 LKLSEDTLYS-QTMT-VPYTYAGVFFS------GFHGMPYGAVPPPVPAVPHNTAAHYGPNM-GGRKFQNNKVLLPWPLN 260 (291)
Q Consensus 190 ~~l~e~~~~~-~~~~-~~~~~~g~~~~------~~~g~p~~~~~p~~~~~~~~~~~~~~~~~-~~~~~~~~~~~i~iP~~ 260 (291)
.+|+++.+.+ ..++ ....-+++..+ +.++++++..+|.+ .+| .++.. .+..+....+.|+||+.
T Consensus 348 kKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~---v~~----a~p~~~~hq~pe~e~V~~fiP~~ 420 (584)
T KOG2193|consen 348 KKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSP---VTF----ASPYPLFHQNPEQEQVRMFIPAQ 420 (584)
T ss_pred HHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCc---ccc----CCCchhhhcCcchhheeeeccHH
Confidence 9999986544 2222 12122333222 12222222111111 111 11111 12344566799999999
Q ss_pred CcceeEEeecCccceehccccccceEEee
Q 022837 261 PVGMLLIILIAQPIICHFSLSIYEEIRLN 289 (291)
Q Consensus 261 ~vG~iIG~~~gg~~ik~~~~~tga~i~~~ 289 (291)
.||+|||+ .|.+||+|.+++||.|+|.
T Consensus 421 ~vGAiIGk--kG~hIKql~RfagASiKIa 447 (584)
T KOG2193|consen 421 AVGAIIGK--KGQHIKQLSRFAGASIKIA 447 (584)
T ss_pred HHHHHHhh--cchhHHHHHHhccceeeec
Confidence 99999999 9999999999999999985
No 4
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.3e-32 Score=232.74 Aligned_cols=241 Identities=24% Similarity=0.332 Sum_probs=183.7
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE 112 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~ 112 (291)
..+.+|+|+.+..+|+||||+|++||.|+.++++.|+|++.+ ..+|+++|+...+.|.+-++.|+-.|.+.+.
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~-----~peri~tisad~~ti~~ilk~iip~lee~f~-- 118 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS-----GPERILTISADIETIGEILKKIIPTLEEGFQ-- 118 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC-----CCceeEEEeccHHHHHHHHHHHhhhhhhCCC--
Confidence 358999999999999999999999999999999999998764 5799999999999888888877766655432
Q ss_pred cccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837 113 DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192 (291)
Q Consensus 113 ~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l 192 (291)
....+.++|+|+.+++|.|||++|+.||+|+++..|+++|... .++.+++|+|.|.|.+..|..+++.|++.|
T Consensus 119 -----~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~--c~p~stdrv~l~~g~~k~v~~~i~~il~~i 191 (390)
T KOG2192|consen 119 -----LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE--CCPHSTDRVVLIGGKPKRVVECIKIILDLI 191 (390)
T ss_pred -----CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc--cCCCCcceEEEecCCcchHHHHHHHHHHHh
Confidence 2455899999999999999999999999999999999999863 568899999999999999999999999999
Q ss_pred hcCcccC------CC-CCCCccCCCccc--CCCCCCCCCCCCCC-C--CCCCC---------------------------
Q 022837 193 SEDTLYS------QT-MTVPYTYAGVFF--SGFHGMPYGAVPPP-V--PAVPH--------------------------- 233 (291)
Q Consensus 193 ~e~~~~~------~~-~~~~~~~~g~~~--~~~~g~p~~~~~p~-~--~~~~~--------------------------- 233 (291)
.|.|.+. +. ....+.|+|..+ ....+.|.+.+.+. + |++++
T Consensus 192 ~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~det 271 (390)
T KOG2192|consen 192 SESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADET 271 (390)
T ss_pred hcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCcccccccccccccc
Confidence 9987533 11 123456776532 22222222111110 0 01100
Q ss_pred ----------------CC---CCC--------CCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceE
Q 022837 234 ----------------NT---AAH--------YGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEI 286 (291)
Q Consensus 234 ----------------~~---~~~--------~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i 286 (291)
|. +.. ||+.+.. ...-.+.++.||.++-|.|||| ||..||||++++||+|
T Consensus 272 w~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdl-GGPitTaQvtip~dlggsiigk--ggqri~~ir~esGA~I 348 (390)
T KOG2192|consen 272 WPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDL-GGPITTAQVTIPKDLGGSIIGK--GGQRIKQIRHESGASI 348 (390)
T ss_pred CCCcCCCcCccccccccCCCCCCCCCccccccccccCCC-CCceeeeeEecccccCcceecc--cchhhhhhhhccCceE
Confidence 00 000 1111111 1223458999999999999999 9999999999999999
Q ss_pred Eeec
Q 022837 287 RLNE 290 (291)
Q Consensus 287 ~~~~ 290 (291)
+|.+
T Consensus 349 kide 352 (390)
T KOG2192|consen 349 KIDE 352 (390)
T ss_pred EecC
Confidence 9976
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=3.4e-32 Score=254.45 Aligned_cols=214 Identities=23% Similarity=0.319 Sum_probs=171.4
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE 112 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~ 112 (291)
..++.+..||...||+||||+|+.|..|+.++||+|++..... +..+|.+.++|.+++|+.|+.||-+++.+.....
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s---~~~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~ 128 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPS---GIGYRSVDLTGSPENVEVAKQLIGEVVSRGRPPG 128 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCC---CcccccccccCCcccHHHHHHhhhhhhhccCCCC
Confidence 4467889999999999999999999999999999999876542 4578999999999999999999987765542111
Q ss_pred -cccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 022837 113 -DQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK 191 (291)
Q Consensus 113 -~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~ 191 (291)
-..+.....++.+|+||++.||+||||+|++||+|++++||++.+..+.....+ .++.+.|+|++++|+.|..||.++
T Consensus 129 ~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~di 207 (600)
T KOG1676|consen 129 GFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADI 207 (600)
T ss_pred CccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHH
Confidence 011122456899999999999999999999999999999999999885543333 789999999999999999999999
Q ss_pred HhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecC
Q 022837 192 LSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIA 271 (291)
Q Consensus 192 l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~g 271 (291)
|+|.-..... + ..+|++ +.....+.+|.||...||.|||| |
T Consensus 208 l~e~~~~~~g-----~-----------------------~~~~g~---------~~g~~~~~~V~VPr~~VG~IIGk--g 248 (600)
T KOG1676|consen 208 LREEDDEVPG-----S-----------------------GGHAGV---------RGGGSATREVKVPRSKVGIIIGK--G 248 (600)
T ss_pred HHhcccCCCc-----c-----------------------ccccCc---------CccccceeEEeccccceeeEEec--C
Confidence 9973211100 0 001111 01122369999999999999999 9
Q ss_pred ccceehccccccceEEee
Q 022837 272 QPIICHFSLSIYEEIRLN 289 (291)
Q Consensus 272 g~~ik~~~~~tga~i~~~ 289 (291)
|++||.|+.+||++|||-
T Consensus 249 GE~IKklq~etG~KIQfk 266 (600)
T KOG1676|consen 249 GEMIKKLQNETGAKIQFK 266 (600)
T ss_pred chHHHHHhhccCceeEee
Confidence 999999999999999984
No 6
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=1.3e-30 Score=246.49 Aligned_cols=241 Identities=26% Similarity=0.372 Sum_probs=180.8
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec---------CHHHHHHHHHHHHH
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG---------TIDEILRAVDLVID 103 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G---------~~~~v~~A~~~I~~ 103 (291)
...++|+||+...+|.||||+|.+||+|+++|.++|+|... .+++.+|+++|+| ..+++.+|.++|..
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~---~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~ 117 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES---LPGCPERIITITGNRVELNLSPATDALFKAFDMIVF 117 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC---CCCCCcceEEEecccccccCCchHHHHHHHHHHHhh
Confidence 33449999999999999999999999999999999999754 5799999999999 99999999999997
Q ss_pred HHhhhhccccccC-CCCC-ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHH
Q 022837 104 KLLTELHAEDQAD-DVGT-KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQ 181 (291)
Q Consensus 104 ~i~~~~~~~~~~~-~~~~-~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v 181 (291)
.+.++.....+.. +.+. .++++|+||.+++|+||||+|+.||+|+++|||+|++.++ .+|...+|.|+|.|.+++|
T Consensus 118 ~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av 195 (485)
T KOG2190|consen 118 KLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAV 195 (485)
T ss_pred cccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHH
Confidence 7664433332222 2222 4899999999999999999999999999999999999985 6788899999999999999
Q ss_pred HHHHHHHHHHHhcCcccCCCCC-CCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCeEEEeecC
Q 022837 182 MRALELILLKLSEDTLYSQTMT-VPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAH-YGPNMGGRKFQNNKVLLPWPL 259 (291)
Q Consensus 182 ~~A~~~I~~~l~e~~~~~~~~~-~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~-~~~~~~~~~~~~~~~~i~iP~ 259 (291)
.+|+..|..+|.+++...+... ....|.. +..++.|.- | ..+..+. +...+........-..+.+|.
T Consensus 196 ~~al~~Is~~L~~~~~~~~~~~~st~~y~P---~~~~~~~~~---~-----s~~~~~~~~~~~~~~~~~~e~~~~~~~p~ 264 (485)
T KOG2190|consen 196 KKALVQISSRLLENPPRSPPPLVSTIPYRP---SASQGGPVL---P-----STAQTSPDAHPFGGIVPEEELVFKLICPS 264 (485)
T ss_pred HHHHHHHHHHHHhcCCcCCCCCCCcccCCC---cccccCccc---c-----ccccCCcccccccccccchhhhhhhcCch
Confidence 9999999999999764421100 0111110 000000000 0 0000000 001111112222336789999
Q ss_pred CCcceeEEeecCccceehccccccceEEeecC
Q 022837 260 NPVGMLLIILIAQPIICHFSLSIYEEIRLNEC 291 (291)
Q Consensus 260 ~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~~ 291 (291)
+.++.|||+ +|..|+.+++++|+.|.++++
T Consensus 265 ~~~~~v~g~--~~~~i~~l~~~~~~~i~v~~~ 294 (485)
T KOG2190|consen 265 DKVGSVIGK--GGLVIRALRNETGASISVGDS 294 (485)
T ss_pred hhceeeecC--CCccchhhhhhcCCceEeccc
Confidence 999999999 999999999999999999874
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=5.7e-30 Score=229.89 Aligned_cols=213 Identities=22% Similarity=0.361 Sum_probs=181.1
Q ss_pred CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837 29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE 108 (291)
Q Consensus 29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~ 108 (291)
+....++++|++..+..||++|||.|.+||+|+++||++|.|++-.+..-...||.|+|.|+.++|.+|..+|+.+|.+.
T Consensus 274 ~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~ 353 (584)
T KOG2193|consen 274 DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLREC 353 (584)
T ss_pred cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHH
Confidence 44567899999999999999999999999999999999999998777655668999999999999999999999999887
Q ss_pred hccccc-------------------------cC-------------------CCCCceEEEEEecCCccceeeccCChhH
Q 022837 109 LHAEDQ-------------------------AD-------------------DVGTKTKLRLIVPNSSCGSIIGKAGATI 144 (291)
Q Consensus 109 ~~~~~~-------------------------~~-------------------~~~~~~~~~i~VP~~~vg~IIGk~G~~I 144 (291)
++.+-. .. .......++|+||...+|+|||++|.+|
T Consensus 354 yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hI 433 (584)
T KOG2193|consen 354 YENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHI 433 (584)
T ss_pred HhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhH
Confidence 554300 00 0124467899999999999999999999
Q ss_pred HHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCC
Q 022837 145 KSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAV 224 (291)
Q Consensus 145 k~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~ 224 (291)
|.|.+.+||.|+|.+.+ .++..+|.|+|+|++++..+|.-.|..+|.|...+.+.-.
T Consensus 434 Kql~RfagASiKIappE--~pdvseRMViItGppeaqfKAQgrifgKikEenf~~Pkee--------------------- 490 (584)
T KOG2193|consen 434 KQLSRFAGASIKIAPPE--IPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKEE--------------------- 490 (584)
T ss_pred HHHHHhccceeeecCCC--CCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCchhh---------------------
Confidence 99999999999998844 3567899999999999999999999999998543321100
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceEEeec
Q 022837 225 PPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNE 290 (291)
Q Consensus 225 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~ 290 (291)
=--.+.+.||...+|.|||| ||.+++.|+.-|+|.+.|++
T Consensus 491 ------------------------vklethirVPs~~aGRvIGK--GGktVnELQnlt~AeV~vPr 530 (584)
T KOG2193|consen 491 ------------------------VKLETHIRVPSSAAGRVIGK--GGKTVNELQNLTSAEVVVPR 530 (584)
T ss_pred ------------------------heeeeeeeccchhhhhhhcc--ccccHHHHhccccceEEccc
Confidence 00127889999999999999 99999999999999999986
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.90 E-value=2.4e-23 Score=197.22 Aligned_cols=201 Identities=26% Similarity=0.414 Sum_probs=153.7
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccc
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAED 113 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~ 113 (291)
++++|||||..++|.||||+|+.||+|+++|||+|++..+ .+|.+++|.|+|.|.++.|.+|+..|...|.+......
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~--~lP~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~ 214 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD--MLPNSTERAVTISGEPDAVKKALVQISSRLLENPPRSP 214 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC--CCCcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCC
Confidence 6899999999999999999999999999999999999985 78999999999999999999999999999988531110
Q ss_pred c--------------cC-------------------CCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 114 Q--------------AD-------------------DVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 114 ~--------------~~-------------------~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
. .. ....+...++..|.+.++.|||++|..|+.|+.++|+.|.+...
T Consensus 215 ~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~ 294 (485)
T KOG2190|consen 215 PPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDS 294 (485)
T ss_pred CCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccc
Confidence 0 00 00123346788999999999999999999999999999999763
Q ss_pred CCCCCCCCceEEEEEcC--HHHH----HHHHHHHHHHHhcCcccCCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCC
Q 022837 161 DHSYYGLNDRLVTLTGT--LDEQ----MRALELILLKLSEDTLYSQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHN 234 (291)
Q Consensus 161 ~~~~~~~~er~V~I~G~--~~~v----~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~ 234 (291)
. .+++|+++.. ++.. ..|..++...+.+.
T Consensus 295 ~------~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~--------------------------------------- 329 (485)
T KOG2190|consen 295 R------TDRIVTISARENPEDRYSMAQEALLLVQPRISEN--------------------------------------- 329 (485)
T ss_pred c------CcceeeeccccCcccccccchhhhhhcccccccc---------------------------------------
Confidence 2 2277777653 1110 11111111111110
Q ss_pred CCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccccceEEeecC
Q 022837 235 TAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLNEC 291 (291)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~~~ 291 (291)
.+... ....+.+|+||++.+|+|||| +|.+|..|++.|||.|+|.++
T Consensus 330 -------~~~~~-~~~v~~~l~vps~~igciiGk--~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 330 -------AGDDL-TQTVTQRLLVPSDLIGCIIGK--GGAKISEIRQRTGASISILNK 376 (485)
T ss_pred -------ccccc-cceeeeeeccCccccceeecc--cccchHHHHHhcCCceEEccc
Confidence 00011 334568999999999999999 999999999999999999753
No 9
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.87 E-value=1.8e-21 Score=166.32 Aligned_cols=160 Identities=31% Similarity=0.540 Sum_probs=136.7
Q ss_pred CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhh
Q 022837 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTEL 109 (291)
Q Consensus 30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~ 109 (291)
....++.+||||+.+++|.|||++|+.||+|++++.+++++.. +..|++++|+|.+.|.+.+|..+++.|++.|.+..
T Consensus 118 ~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift--~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~p 195 (390)
T KOG2192|consen 118 QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFT--ECCPHSTDRVVLIGGKPKRVVECIKIILDLISESP 195 (390)
T ss_pred CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhh--ccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCC
Confidence 3445689999999999999999999999999999999999975 67899999999999999999999999998775441
Q ss_pred ccc--------------c---------c---------------------------------c------------------
Q 022837 110 HAE--------------D---------Q---------------------------------A------------------ 115 (291)
Q Consensus 110 ~~~--------------~---------~---------------------------------~------------------ 115 (291)
-.. + + .
T Consensus 196 ikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~sa 275 (390)
T KOG2192|consen 196 IKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSA 275 (390)
T ss_pred cCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCc
Confidence 000 0 0 0
Q ss_pred ---------------------------------CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCC
Q 022837 116 ---------------------------------DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDH 162 (291)
Q Consensus 116 ---------------------------------~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~ 162 (291)
.......+.++.||.+.-|.||||+|+.|++|+.++||.|++..
T Consensus 276 idtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikide--- 352 (390)
T KOG2192|consen 276 IDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDE--- 352 (390)
T ss_pred CCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecC---
Confidence 00134568899999999999999999999999999999999976
Q ss_pred CCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 163 SYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 163 ~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
.+.++.||+++|+|+.++++.|..+++..++.
T Consensus 353 pleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 353 PLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred cCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 44577899999999999999999999988874
No 10
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=8.3e-21 Score=166.49 Aligned_cols=132 Identities=23% Similarity=0.293 Sum_probs=112.6
Q ss_pred CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS 199 (291)
Q Consensus 120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~ 199 (291)
....++++||+..+|.||||+|++|.+|+.+|||+|++++..++.|+.+||+|.|+|+.+++....+.|.++|+|.+...
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~ 116 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAV 116 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhh
Confidence 34899999999999999999999999999999999999999999999999999999999999999999999999976543
Q ss_pred CCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcc
Q 022837 200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFS 279 (291)
Q Consensus 200 ~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~ 279 (291)
......+ -|+ ...+...+.|.||+...|.|||| ||.+||.++
T Consensus 117 ~k~v~~~------------~pq------------------------t~~r~kqikivvPNstag~iigk--ggAtiK~~~ 158 (402)
T KOG2191|consen 117 AKPVDIL------------QPQ------------------------TPDRIKQIKIVVPNSTAGMIIGK--GGATIKAIQ 158 (402)
T ss_pred cCCcccc------------CCC------------------------CccccceeEEeccCCcccceecC--CcchHHHHH
Confidence 2211000 000 01122348999999999999999 999999999
Q ss_pred ccccceEEee
Q 022837 280 LSIYEEIRLN 289 (291)
Q Consensus 280 ~~tga~i~~~ 289 (291)
+++||.|||.
T Consensus 159 Eqsga~iqis 168 (402)
T KOG2191|consen 159 EQSGAWIQIS 168 (402)
T ss_pred HhhCcceEec
Confidence 9999999986
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=99.79 E-value=6.6e-19 Score=146.84 Aligned_cols=139 Identities=17% Similarity=0.227 Sum_probs=107.4
Q ss_pred EEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEE---ecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMI---SGTIDEILRAVDLVIDKLLTELHAEDQA 115 (291)
Q Consensus 39 ilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I---~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (291)
|.||.+.+|.|||++|++|+.|+++||++|++.++ +..|.| +++++++.+|+++|....... ..++..
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~ 72 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGF-SPEKAL 72 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCC-CHHHHH
Confidence 56899999999999999999999999999999753 245777 789999999999998644321 111000
Q ss_pred CCCCCceE-EEEEecC---------CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHH
Q 022837 116 DDVGTKTK-LRLIVPN---------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRAL 185 (291)
Q Consensus 116 ~~~~~~~~-~~i~VP~---------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~ 185 (291)
....+... ..+.|+. ..+|+|||++|++++.|++.|||+|.|.. +.|.|.|++++++.|+
T Consensus 73 ~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~ 142 (172)
T TIGR03665 73 KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAR 142 (172)
T ss_pred HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHH
Confidence 00011112 2233433 36899999999999999999999999963 6799999999999999
Q ss_pred HHHHHHHhcCc
Q 022837 186 ELILLKLSEDT 196 (291)
Q Consensus 186 ~~I~~~l~e~~ 196 (291)
.+|.+++.+.+
T Consensus 143 ~~i~~li~~~~ 153 (172)
T TIGR03665 143 EAIEMLIEGAP 153 (172)
T ss_pred HHHHHHHcCCC
Confidence 99999997654
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.76 E-value=7.8e-18 Score=141.30 Aligned_cols=142 Identities=18% Similarity=0.222 Sum_probs=109.1
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEe----cCHHHHHHHHHHHHHHHhh-hh
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMIS----GTIDEILRAVDLVIDKLLT-EL 109 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~----G~~~~v~~A~~~I~~~i~~-~~ 109 (291)
+...+.||.+.+|.|||++|++|+.|+++||++|++..+ +..|.|. ++++++.+|+++|.+.+.. ..
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 467899999999999999999999999999999999753 2557774 8999999999999865542 11
Q ss_pred ccccccCCCCCceEEEE-Eec---------CCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHH
Q 022837 110 HAEDQADDVGTKTKLRL-IVP---------NSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD 179 (291)
Q Consensus 110 ~~~~~~~~~~~~~~~~i-~VP---------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~ 179 (291)
+.. .....+....++ .+. ...+|+|||++|++++.|++.|||+|.|.. +.|.|.|+++
T Consensus 75 e~A--~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~----------~~v~i~G~~~ 142 (180)
T PRK13763 75 EKA--LRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG----------KTVAIIGDPE 142 (180)
T ss_pred HHH--HHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------CEEEEEeCHH
Confidence 100 000011112121 111 136899999999999999999999999964 3499999999
Q ss_pred HHHHHHHHHHHHHhcCc
Q 022837 180 EQMRALELILLKLSEDT 196 (291)
Q Consensus 180 ~v~~A~~~I~~~l~e~~ 196 (291)
+++.|...|..+++...
T Consensus 143 ~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 143 QVEIAREAIEMLIEGAP 159 (180)
T ss_pred HHHHHHHHHHHHHcCCC
Confidence 99999999999997653
No 13
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.57 E-value=8.3e-15 Score=102.62 Aligned_cols=64 Identities=42% Similarity=0.772 Sum_probs=59.2
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I 101 (291)
++||+||.+.+|+||||+|.+|++|+++|||+|++.+..+ ++..+|+|+|.|+++++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence 4799999999999999999999999999999999987653 467899999999999999999987
No 14
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.56 E-value=1.2e-14 Score=101.86 Aligned_cols=65 Identities=45% Similarity=0.671 Sum_probs=58.8
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~ 189 (291)
+++|+||.+++|+|||++|++|++|+++|||+|++.+... ++..+|.|+|+|+++++.+|+.+|.
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 3689999999999999999999999999999999987543 3567899999999999999999873
No 15
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.52 E-value=2.8e-14 Score=133.19 Aligned_cols=241 Identities=24% Similarity=0.285 Sum_probs=168.7
Q ss_pred CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837 29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE 108 (291)
Q Consensus 29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~ 108 (291)
....+++.+++.|+...|-+++||.|.+|+.|++.++++|.+..++- ..++..++.|-+..+..|+..+++++.+.
T Consensus 62 ~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 62 QKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred cCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence 44557799999999999999999999999999999999999976542 35677778888999999999998777654
Q ss_pred hccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 022837 109 LHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI 188 (291)
Q Consensus 109 ~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I 188 (291)
..+...+-+|...+++|+|++|.+++.|+.-++|+|.+...- .....+...|.|...-+..|..++
T Consensus 138 -----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~g~~~~~~i~~qqk~~~~a~~~~ 203 (608)
T KOG2279|consen 138 -----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RLGLSRLIKISGQQKEVAAAKHLI 203 (608)
T ss_pred -----------Ccccccccchhhhcccccccchhhhcchhccccccccccccc---ccccccceecccccchHHHHHhhh
Confidence 346778889999999999999999999999999999998742 233578889999988899999999
Q ss_pred HHHHhcCcccCCCC----------CCCccC--CCcccCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC---C-CCCCC-
Q 022837 189 LLKLSEDTLYSQTM----------TVPYTY--AGVFFSGFHGMPYGAVPPPVPAVPHNTAAH--YGPNM---G-GRKFQ- 249 (291)
Q Consensus 189 ~~~l~e~~~~~~~~----------~~~~~~--~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~--~~~~~---~-~~~~~- 249 (291)
.+.+.++......+ ..+.+- .++..+...+.|.--..-.....++.++.. .++.. . .+.++
T Consensus 204 ~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~ 283 (608)
T KOG2279|consen 204 LEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEK 283 (608)
T ss_pred hccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCC
Confidence 99988763211111 011111 111112222222111100001111111111 11110 0 00111
Q ss_pred --CC---------eEEEeecCCCcceeEEeecCccceehccccccceEEee
Q 022837 250 --NN---------KVLLPWPLNPVGMLLIILIAQPIICHFSLSIYEEIRLN 289 (291)
Q Consensus 250 --~~---------~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tga~i~~~ 289 (291)
.. ..+|.+|.-.+|.+||+ .|+.++.++..+++.++|-
T Consensus 284 ~~d~s~~k~~~l~i~e~e~p~~lsg~lig~--~gey~s~yssasn~~~hi~ 332 (608)
T KOG2279|consen 284 PSDDSFQKSEALAIPEMEMPEILSGDLIGH--AGEYLSVYSSASNHPNHIW 332 (608)
T ss_pred ccccccccccccccceeecCcccccchhhh--hhhhhhhhhhccCccceEE
Confidence 11 17889999999999999 9999999999999999874
No 16
>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=99.40 E-value=1.1e-13 Score=115.38 Aligned_cols=111 Identities=14% Similarity=0.078 Sum_probs=84.6
Q ss_pred EEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE---EcCHHHHHHHHHHHHHHHhcC-cccCC-
Q 022837 126 LIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL---TGTLDEQMRALELILLKLSED-TLYSQ- 200 (291)
Q Consensus 126 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I---~G~~~~v~~A~~~I~~~l~e~-~~~~~- 200 (291)
+.||.+.+|.|||++|++||+|+++|||+|++.. ++..|.| +++++++.+|+.+|..+.... +....
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~--------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~ 73 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALK 73 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 5689999999999999999999999999999986 2357888 789999999999999987752 11000
Q ss_pred CCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeec---------CCCcceeEEeecC
Q 022837 201 TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWP---------LNPVGMLLIILIA 271 (291)
Q Consensus 201 ~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP---------~~~vG~iIG~~~g 271 (291)
.+.. .|.+ .-+.|+ ...+|.|||+ |
T Consensus 74 l~gd--~y~~------------------------------------------~Vi~I~~~~~~~~~~~~~~griIG~--~ 107 (172)
T TIGR03665 74 LLDD--DYML------------------------------------------EVIDLKEYGKSPNALRRIKGRIIGE--G 107 (172)
T ss_pred hcCC--cceE------------------------------------------EEEEhhhccCCHHHHHHHHhhhcCC--C
Confidence 0000 0000 001111 1369999999 9
Q ss_pred ccceehccccccceEEeec
Q 022837 272 QPIICHFSLSIYEEIRLNE 290 (291)
Q Consensus 272 g~~ik~~~~~tga~i~~~~ 290 (291)
|.+++.|+..|||+|.|.+
T Consensus 108 G~t~~~ie~~t~~~i~i~~ 126 (172)
T TIGR03665 108 GKTRRIIEELTGVSISVYG 126 (172)
T ss_pred cHHHHHHHHHHCCeEEEcC
Confidence 9999999999999999975
No 17
>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=99.40 E-value=4.8e-13 Score=92.72 Aligned_cols=61 Identities=26% Similarity=0.404 Sum_probs=55.8
Q ss_pred EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (291)
Q Consensus 124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~ 189 (291)
.++.||..++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|..|+.+|.
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 57899999999999999999999999999999999743 36789999999999999999873
No 18
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.39 E-value=3.7e-13 Score=113.07 Aligned_cols=124 Identities=13% Similarity=0.075 Sum_probs=88.5
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE----cCHHHHHHHHHHHHHHHhc-Cc
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT----GTLDEQMRALELILLKLSE-DT 196 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~----G~~~~v~~A~~~I~~~l~e-~~ 196 (291)
....+.||.+.+|.|||++|++||.|+++|||+|++.. ++..|.|. ++++++++|+++|..++.. ++
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 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFSP 74 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCCH
Confidence 46789999999999999999999999999999999986 23678885 8999999999999998875 22
Q ss_pred ccCC-CCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccce
Q 022837 197 LYSQ-TMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPII 275 (291)
Q Consensus 197 ~~~~-~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~i 275 (291)
.... .... .|.+-... ...| +.+. + .....+|.|||+ ||.++
T Consensus 75 e~A~~l~gd--~y~~~Vi~----------------i~~~-----~~~~-------~-----~~~r~~griIG~--~G~~~ 117 (180)
T PRK13763 75 EKALRLLDD--DYVLEVID----------------LSDY-----GDSP-------N-----ALRRIKGRIIGE--GGKTR 117 (180)
T ss_pred HHHHHHhCC--CceEEEEE----------------hhhc-----cCCh-------h-----HHHHHhhheeCC--CcHHH
Confidence 2000 0000 01100000 0000 0000 0 011369999999 99999
Q ss_pred ehccccccceEEeec
Q 022837 276 CHFSLSIYEEIRLNE 290 (291)
Q Consensus 276 k~~~~~tga~i~~~~ 290 (291)
+.|++.|||+|+|.+
T Consensus 118 k~ie~~t~~~i~i~~ 132 (180)
T PRK13763 118 RIIEELTGVDISVYG 132 (180)
T ss_pred HHHHHHHCcEEEEcC
Confidence 999999999999976
No 19
>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=99.38 E-value=4e-13 Score=92.49 Aligned_cols=60 Identities=32% Similarity=0.520 Sum_probs=54.9
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI 188 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I 188 (291)
|.+|.||.+++|+|||++|++|++|+++|||+|+|+++ + .+..|+|+|++++|++|+.+|
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 57899999999999999999999999999999999863 2 456999999999999999986
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=99.37 E-value=7.4e-13 Score=91.12 Aligned_cols=60 Identities=30% Similarity=0.577 Sum_probs=54.6
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I 101 (291)
+.+|+||.+++|+|||++|.+|++|+++|||+|+|+++ + .+..|+|+|++++|.+|+++|
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 57899999999999999999999999999999999764 2 345999999999999999886
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.36 E-value=2.7e-12 Score=88.54 Aligned_cols=58 Identities=22% Similarity=0.396 Sum_probs=53.2
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELI 188 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I 188 (291)
....+.||.+++|+||||+|++||+|+++|||+|.++. ++.|.|+|+ .+++++|+++|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHh
Confidence 46778999999999999999999999999999999975 357999999 99999999987
No 22
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.34 E-value=1.8e-12 Score=89.82 Aligned_cols=61 Identities=21% Similarity=0.415 Sum_probs=55.8
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~ 102 (291)
.+|.||..++|.|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|..|+.+|+
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 57899999999999999999999999999999998753 46789999999999999998873
No 23
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.34 E-value=5.9e-12 Score=87.51 Aligned_cols=62 Identities=45% Similarity=0.663 Sum_probs=56.3
Q ss_pred EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 022837 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELI 188 (291)
Q Consensus 124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I 188 (291)
.++.||.+++++|||++|++|++|+++|||+|.|.+... ...++.|+|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHh
Confidence 579999999999999999999999999999999987432 34789999999999999999887
No 24
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.31 E-value=9.9e-12 Score=86.37 Aligned_cols=62 Identities=40% Similarity=0.756 Sum_probs=56.6
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHH
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLV 101 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I 101 (291)
.+|.||..++++|||++|++|++|+++|||+|.|+...+ ...++.|.|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHh
Confidence 689999999999999999999999999999999987543 45789999999999999998876
No 25
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.28 E-value=1.6e-11 Score=84.71 Aligned_cols=58 Identities=21% Similarity=0.388 Sum_probs=52.8
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHH
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLV 101 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I 101 (291)
....|.||.+.+|+||||+|++|++|+++|||+|++++ ++.|.|+|+ .++++.|+++|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHh
Confidence 46789999999999999999999999999999999964 356999998 89999999887
No 26
>PF13014 KH_3: KH domain
Probab=99.15 E-value=8.5e-11 Score=75.21 Aligned_cols=43 Identities=44% Similarity=0.661 Sum_probs=38.4
Q ss_pred ccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc
Q 022837 132 SCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG 176 (291)
Q Consensus 132 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G 176 (291)
++|+|||++|++|++|+++|||+|+|++ ...++..++.|+|+|
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 5899999999999999999999999998 234566899999998
No 27
>PF13014 KH_3: KH domain
Probab=99.13 E-value=1.2e-10 Score=74.47 Aligned_cols=43 Identities=44% Similarity=0.890 Sum_probs=38.8
Q ss_pred ccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89 (291)
Q Consensus 45 ~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G 89 (291)
++|+||||+|.+|++|+++|||+|+|++ +..++..+|.|+|+|
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 5899999999999999999999999998 344677899999987
No 28
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.10 E-value=1.9e-09 Score=89.77 Aligned_cols=146 Identities=16% Similarity=0.234 Sum_probs=107.8
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-----CHHHHHHHHHHHHHHHhh
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-----TIDEILRAVDLVIDKLLT 107 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-----~~~~v~~A~~~I~~~i~~ 107 (291)
......+.||.+..+.+||+.|++.+.|++.++++|.+.. .+..|.|.- .|-.+.+|.+.|. .+..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--------~~~~V~i~~~~~t~Dp~~~~ka~d~Vk-AIgr 76 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--------KTGSVTIRTTRKTEDPLALLKARDVVK-AIGR 76 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--------CCCeEEEEecCCCCChHHHHHHHHHHH-HHhc
Confidence 3456779999999999999999999999999999999964 345666654 4678888988885 3333
Q ss_pred hhccccccCCCCCceEEEE-E-----e-cC----CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEc
Q 022837 108 ELHAEDQADDVGTKTKLRL-I-----V-PN----SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTG 176 (291)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~i-~-----V-P~----~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G 176 (291)
-+..+....-..+...+.+ . - +. ...|+|||++|.+.+.|++-|||.|.|.. .+|.|-|
T Consensus 77 GF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG 146 (194)
T COG1094 77 GFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIG 146 (194)
T ss_pred CCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEec
Confidence 2221100000000111111 1 1 11 24589999999999999999999999975 5899999
Q ss_pred CHHHHHHHHHHHHHHHhcCcc
Q 022837 177 TLDEQMRALELILLKLSEDTL 197 (291)
Q Consensus 177 ~~~~v~~A~~~I~~~l~e~~~ 197 (291)
.+++|+.|++.|..++...++
T Consensus 147 ~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 147 GFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred ChhhhHHHHHHHHHHHcCCCc
Confidence 999999999999999988664
No 29
>smart00322 KH K homology RNA-binding domain.
Probab=99.10 E-value=7.1e-10 Score=77.27 Aligned_cols=67 Identities=33% Similarity=0.547 Sum_probs=60.2
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~ 193 (291)
.+.++.||..+++.+||++|++|++|++.||++|.+..... ....|+|.|+.+++..|..+|.+.++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-----~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-----EERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-----CccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999976321 56889999999999999999998763
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=99.05 E-value=1.8e-09 Score=75.23 Aligned_cols=67 Identities=30% Similarity=0.658 Sum_probs=59.6
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHH
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKL 105 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i 105 (291)
.+..+|.||...+|.+||++|.+|++|++.||++|.+.... .....+.|.|..+++..|..+|.+.+
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 46789999999999999999999999999999999997543 25688999999999999999998654
No 31
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.77 E-value=2.4e-08 Score=100.47 Aligned_cols=201 Identities=19% Similarity=0.230 Sum_probs=148.1
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCC--CCceEEEEecCHHHHHHHHHHHHHHHhhh-
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPG--TTDRIIMISGTIDEILRAVDLVIDKLLTE- 108 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~--~~er~v~I~G~~~~v~~A~~~I~~~i~~~- 108 (291)
..-+..++.+......++||++|.+++.++.++.+.+.++..++..+. ...+...+....-++..+..++..-+..+
T Consensus 198 ~r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~ 277 (753)
T KOG2208|consen 198 ERSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDE 277 (753)
T ss_pred ceeEEEEeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhh
Confidence 344889999999999999999999999999999999999865542111 12233334444445555555442211000
Q ss_pred -----hc-------------------cc----cc---c-------------------------CCCCCceEEEEEecCCc
Q 022837 109 -----LH-------------------AE----DQ---A-------------------------DDVGTKTKLRLIVPNSS 132 (291)
Q Consensus 109 -----~~-------------------~~----~~---~-------------------------~~~~~~~~~~i~VP~~~ 132 (291)
++ .. .. . .-........+.+-...
T Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~ 357 (753)
T KOG2208|consen 278 IIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEE 357 (753)
T ss_pred hhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHh
Confidence 00 00 00 0 00123367788889999
Q ss_pred cceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCCCCCccCCCcc
Q 022837 133 CGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTMTVPYTYAGVF 212 (291)
Q Consensus 133 vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~~~~~~~g~~ 212 (291)
+..++||+|.+|.+|++++.|.|.+... +..+..|.++|....+.+|...+...+.+-.+-
T Consensus 358 ~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~-------------- 418 (753)
T KOG2208|consen 358 LKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILNS-------------- 418 (753)
T ss_pred hhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhcc--------------
Confidence 9999999999999999999999999873 346788999999999999999999998884321
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccccc-ceEEeec
Q 022837 213 FSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSIY-EEIRLNE 290 (291)
Q Consensus 213 ~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~tg-a~i~~~~ 290 (291)
...-.+.+|...+..+||. ||..|..|+.+.| -+|++.+
T Consensus 419 -------------------------------------~~~~~~~iP~k~~~~iig~--~g~~i~~I~~k~~~v~i~f~~ 458 (753)
T KOG2208|consen 419 -------------------------------------IVKEEVQIPTKSHKRIIGT--KGALINYIMGKHGGVHIKFQN 458 (753)
T ss_pred -------------------------------------cccceeecCccchhhhhcc--ccccHHHHHhhcCcEEEecCC
Confidence 0125678999999999999 9999999999999 7777654
No 32
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.77 E-value=1.3e-08 Score=89.66 Aligned_cols=140 Identities=17% Similarity=0.254 Sum_probs=111.2
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc--
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH-- 110 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~-- 110 (291)
+.++..+.||..+++.|.|++|.+||.|+.+|.+.|+-+... .+.++.++|..++|..|++.|... .+.+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~sa-aeH~~l~ 96 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSA-AEHFGLI 96 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCccc-cceeeee
Confidence 788899999999999999999999999999999999998654 468899999999999999998641 11111
Q ss_pred -------cccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHH-HH
Q 022837 111 -------AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE-QM 182 (291)
Q Consensus 111 -------~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~-v~ 182 (291)
..........+.+...-+|...+|.|.|..|++|+.|++.+...|.-.-. ..+.++.++|-+.. ++
T Consensus 97 ~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~------~~~~Vf~Vtg~~~nC~k 170 (394)
T KOG2113|consen 97 RASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR------CGEPVFCVTGAPKNCVK 170 (394)
T ss_pred eecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc------CCCceEEEecCCcchhh
Confidence 00011123456778888999999999999999999999999988876642 25678889998887 45
Q ss_pred HHH
Q 022837 183 RAL 185 (291)
Q Consensus 183 ~A~ 185 (291)
+|.
T Consensus 171 ra~ 173 (394)
T KOG2113|consen 171 RAR 173 (394)
T ss_pred hcc
Confidence 555
No 33
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.77 E-value=3.3e-08 Score=77.32 Aligned_cols=67 Identities=22% Similarity=0.180 Sum_probs=53.5
Q ss_pred CCccceeeccCChhHHHHHHhccceEEEecCCCCC--------------CCCCceEEEEEcCH---HHHHHHHHHHHHHH
Q 022837 130 NSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSY--------------YGLNDRLVTLTGTL---DEQMRALELILLKL 192 (291)
Q Consensus 130 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~--------------~~~~er~V~I~G~~---~~v~~A~~~I~~~l 192 (291)
.+++|.|||++|.+||+|+++|||+|.|..+.... ...++-.|.|++.. +++.+|+.+|..++
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 46889999999999999999999999998742110 11233579999975 99999999999999
Q ss_pred hcCc
Q 022837 193 SEDT 196 (291)
Q Consensus 193 ~e~~ 196 (291)
....
T Consensus 94 ~~~~ 97 (120)
T cd02395 94 KPAI 97 (120)
T ss_pred ccCC
Confidence 8643
No 34
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.65 E-value=6.6e-08 Score=97.34 Aligned_cols=146 Identities=23% Similarity=0.324 Sum_probs=118.9
Q ss_pred CCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhc
Q 022837 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELH 110 (291)
Q Consensus 31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~ 110 (291)
.+..+.+.+.+-......|+||+|.+|.+|++++.|.|.++.. +..+..+.++|...++.+|.+.+.....+...
T Consensus 343 ~~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-----~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 343 EENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-----GSNNKKVVITGVSANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred hccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-----cCCCCCeEEeccccchhHHHHHHHHHHHhhhc
Confidence 3445888899999999999999999999999999999999873 35678899999999999999999866555421
Q ss_pred cccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhcc-ceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837 111 AEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQ-AVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (291)
Q Consensus 111 ~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG-a~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~ 189 (291)
. .....+.+|...+.++||.+|..|..|.++++ .+|++... ......+++.|....+..+..+..
T Consensus 418 ~---------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-----~~~~~~~~~~~~~~dv~~~~~~~~ 483 (753)
T KOG2208|consen 418 S---------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-----NNSSDMVTIRGISKDVEKSVSLLK 483 (753)
T ss_pred c---------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC-----CcccccceEeccccccchhHHHHH
Confidence 1 35677999999999999999999999999999 66666553 224556888888888877777776
Q ss_pred HHHhcC
Q 022837 190 LKLSED 195 (291)
Q Consensus 190 ~~l~e~ 195 (291)
.+..+.
T Consensus 484 ~~~~~a 489 (753)
T KOG2208|consen 484 ALKADA 489 (753)
T ss_pred hhhhhh
Confidence 665543
No 35
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.64 E-value=8.8e-08 Score=77.05 Aligned_cols=103 Identities=20% Similarity=0.281 Sum_probs=74.3
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA 115 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (291)
.+.|+|+...+|..||++|++|+.|++..|-+|.+-..++ .+..+|...+....-..-..
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~V~~v~I 92 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAAVRSVTI 92 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCEEEEEEE
Confidence 4778899999999999999999999999999998865321 13344443332211000001
Q ss_pred CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEe
Q 022837 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS 158 (291)
Q Consensus 116 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 158 (291)
.+........+.|+.+..|..|||+|++++.++.-+|-++.|.
T Consensus 93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 1112235677789999999999999999999999999887764
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=98.57 E-value=2.9e-07 Score=72.03 Aligned_cols=63 Identities=19% Similarity=0.431 Sum_probs=48.2
Q ss_pred cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCC--------------CCceEEEEecC---HHHHHHHHHHHHHHHh
Q 022837 44 PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPG--------------TTDRIIMISGT---IDEILRAVDLVIDKLL 106 (291)
Q Consensus 44 ~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~--------------~~er~v~I~G~---~~~v~~A~~~I~~~i~ 106 (291)
+.+|.|||++|.+||+|+++|||+|.|........+ ...-.|.|++. .+.+.+|+.+|...+.
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 468999999999999999999999999875211100 12245788875 4899999999986665
No 37
>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=98.49 E-value=8.6e-07 Score=87.94 Aligned_cols=91 Identities=18% Similarity=0.191 Sum_probs=73.8
Q ss_pred HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEE
Q 022837 94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT 173 (291)
Q Consensus 94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~ 173 (291)
+.+|+..|++.+.+.+... .......+....+.||.+++|.|||+||++||+|+++|||+|.|.. +..|.
T Consensus 551 A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~ 620 (719)
T TIGR02696 551 ARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVY 620 (719)
T ss_pred HHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEE
Confidence 3455666777777665544 3333345678889999999999999999999999999999999974 46899
Q ss_pred EEcC-HHHHHHHHHHHHHHHhc
Q 022837 174 LTGT-LDEQMRALELILLKLSE 194 (291)
Q Consensus 174 I~G~-~~~v~~A~~~I~~~l~e 194 (291)
|.+. .+++++|+.+|..++..
T Consensus 621 I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 621 IGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEeCCHHHHHHHHHHHHHhhCc
Confidence 8885 88999999999999885
No 38
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.43 E-value=1.1e-07 Score=89.63 Aligned_cols=113 Identities=23% Similarity=0.295 Sum_probs=96.7
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCccc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLY 198 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~ 198 (291)
...+..++.|+..++-+++||.|.+||.|+..++++|.+..++- ..++.-.+.|.+.++..|+..+.+++.+++..
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pv 140 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDV----GDERVLLISGFPVQVCKAKAAIHQILTENTPV 140 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccC----CcccchhhccCCCCCChHHHHHHHHHhcCCcc
Confidence 45678999999999999999999999999999999999987542 25666777779999999999999999885443
Q ss_pred CCCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehc
Q 022837 199 SQTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHF 278 (291)
Q Consensus 199 ~~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~ 278 (291)
. .++.+|..++++|+|| ||.++..+
T Consensus 141 k-----------------------------------------------------~~lsvpqr~~~~i~gr--gget~~si 165 (608)
T KOG2279|consen 141 S-----------------------------------------------------EQLSVPQRSVGRIIGR--GGETIRSI 165 (608)
T ss_pred c-----------------------------------------------------ccccchhhhccccccc--chhhhcch
Confidence 2 5566788999999999 99999999
Q ss_pred cccccceEEeec
Q 022837 279 SLSIYEEIRLNE 290 (291)
Q Consensus 279 ~~~tga~i~~~~ 290 (291)
...++|.|-+.+
T Consensus 166 ~~ss~aki~~d~ 177 (608)
T KOG2279|consen 166 CKSSGAKITCDK 177 (608)
T ss_pred hccccccccccc
Confidence 999999987654
No 39
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.24 E-value=4.4e-06 Score=83.79 Aligned_cols=91 Identities=13% Similarity=0.150 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE
Q 022837 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL 174 (291)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I 174 (291)
.++...|++.+.+.+...........+....+.||.+.++.|||+||++||+|+++|||+|.|.. +..|.|
T Consensus 524 ~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i 594 (684)
T TIGR03591 524 KEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKI 594 (684)
T ss_pred HHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEE
Confidence 34445566666555443322223344578889999999999999999999999999999999974 356777
Q ss_pred EcC-HHHHHHHHHHHHHHHhc
Q 022837 175 TGT-LDEQMRALELILLKLSE 194 (291)
Q Consensus 175 ~G~-~~~v~~A~~~I~~~l~e 194 (291)
.+. .+.+++|..+|..+..+
T Consensus 595 ~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 595 AASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EECcHHHHHHHHHHHHhhhcc
Confidence 774 78899999999988664
No 40
>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=98.18 E-value=5.3e-06 Score=66.62 Aligned_cols=103 Identities=23% Similarity=0.329 Sum_probs=72.1
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA 115 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (291)
.+-|+|....+|..||++|.+|+.|++..|-+|.+-..+ ..+. ..|...+.-..-..-..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys--------------~D~~------~fI~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS--------------ENLE------EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC--------------CCHH------HHHHHcCCCceEEEEEE
Confidence 677899999999999999999999999999888885432 1121 22222111110000000
Q ss_pred CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEe
Q 022837 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKIS 158 (291)
Q Consensus 116 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 158 (291)
...++.....+.||.+..+..|||+|.|++...+-+|-++.|.
T Consensus 94 ~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 94 SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 1112345677889999999999999999999999998887664
No 41
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.09 E-value=3.6e-05 Score=72.12 Aligned_cols=75 Identities=20% Similarity=0.200 Sum_probs=59.0
Q ss_pred ceEEEEEec------CCccceeeccCChhHHHHHHhccceEEEecCC------------CCCCCCC-ceEEEEEcC-HHH
Q 022837 121 KTKLRLIVP------NSSCGSIIGKAGATIKSFMDDSQAVIKISRLD------------HSYYGLN-DRLVTLTGT-LDE 180 (291)
Q Consensus 121 ~~~~~i~VP------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~------------~~~~~~~-er~V~I~G~-~~~ 180 (291)
..+.++.|| -++||+|||..|.|.|+|+++|||+|.|-.+. ...++.. +=.+.|+++ .+.
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 577888888 56899999999999999999999999997611 0112222 334888887 788
Q ss_pred HHHHHHHHHHHHhcC
Q 022837 181 QMRALELILLKLSED 195 (291)
Q Consensus 181 v~~A~~~I~~~l~e~ 195 (291)
|++|++.|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999864
No 42
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.94 E-value=2.1e-05 Score=79.95 Aligned_cols=91 Identities=14% Similarity=0.127 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccce-EEEecCCCCCCCCCceEEE
Q 022837 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAV-IKISRLDHSYYGLNDRLVT 173 (291)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~~~~~~er~V~ 173 (291)
.+|+..|++.|.+.+...........+....+.||.++++.|||.||.+||.|.++||+. |.+.. +-.|.
T Consensus 658 ~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~ 728 (891)
T PLN00207 658 KDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVK 728 (891)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEE
Confidence 344455666666655433222333456788899999999999999999999999999999 88764 46788
Q ss_pred EEcC-HHHHHHHHHHHHHHHhc
Q 022837 174 LTGT-LDEQMRALELILLKLSE 194 (291)
Q Consensus 174 I~G~-~~~v~~A~~~I~~~l~e 194 (291)
|.+. .+.+++|+++|.++..+
T Consensus 729 I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 729 ITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred EEeCCHHHHHHHHHHHHHHhcC
Confidence 8885 88999999999998874
No 43
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.91 E-value=1.4e-05 Score=70.72 Aligned_cols=126 Identities=19% Similarity=0.190 Sum_probs=92.9
Q ss_pred CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS 199 (291)
Q Consensus 120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~ 199 (291)
..++..+.||..+++.+.|++|.+||.|+.+|...|.-+... .+.++.++|.++.|..|+..|..-- |+....
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saa-eH~~l~ 96 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAA-EHFGLI 96 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCcccc-ceeeee
Confidence 568889999999999999999999999999999998876532 4678999999999999998775421 111000
Q ss_pred CCCCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcc
Q 022837 200 QTMTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFS 279 (291)
Q Consensus 200 ~~~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~ 279 (291)
.|.+. +..+.+++ ..+-+.+.+..+|-..||.|.|- -|.+||.++
T Consensus 97 -------~~s~s-------------------------~Sgg~~~~-s~s~qt~sy~svP~rvvglvv~~--~~~ti~~iq 141 (394)
T KOG2113|consen 97 -------RASRS-------------------------FSGGTNGA-SASGQTTSYVSVPLRVVGLVVGP--KGATIKRIQ 141 (394)
T ss_pred -------eeccc-------------------------ccCCCccc-cccCCCceeeeccceeeeecccc--ccCccchhe
Confidence 01100 00111111 12334568889999999999999 999999999
Q ss_pred ccccceEE
Q 022837 280 LSIYEEIR 287 (291)
Q Consensus 280 ~~tga~i~ 287 (291)
+.+-..|.
T Consensus 142 q~tnt~I~ 149 (394)
T KOG2113|consen 142 QFTNTYIA 149 (394)
T ss_pred ecccceEe
Confidence 99988875
No 44
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.86 E-value=4.4e-05 Score=74.62 Aligned_cols=102 Identities=19% Similarity=0.164 Sum_probs=78.2
Q ss_pred EEEEecCHHH--------HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceE
Q 022837 84 IIMISGTIDE--------ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI 155 (291)
Q Consensus 84 ~v~I~G~~~~--------v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I 155 (291)
-+.|.|.... ...|.-.|+..+.+.+...........+....+.|+.+.++-+||++|++|++|.++|||+|
T Consensus 506 DiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~I 585 (692)
T COG1185 506 DIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKI 585 (692)
T ss_pred eeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEE
Confidence 3777775543 34456667777766654432223334456788889999999999999999999999999999
Q ss_pred EEecCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhc
Q 022837 156 KISRLDHSYYGLNDRLVTLTGTL-DEQMRALELILLKLSE 194 (291)
Q Consensus 156 ~i~~~~~~~~~~~er~V~I~G~~-~~v~~A~~~I~~~l~e 194 (291)
++.. +..|.|.++. +.+.+|+.+|..+.++
T Consensus 586 died---------dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 586 DIED---------DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred EecC---------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 9973 4579999985 8899999999999966
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.80 E-value=9.7e-05 Score=69.32 Aligned_cols=74 Identities=19% Similarity=0.368 Sum_probs=54.5
Q ss_pred cEEEEEEeccc------ccceeeccCChhHHHHHHHhCCcEEEcCCC------------CCCCCC-CceEEEEec-CHHH
Q 022837 34 PTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRSH------------EFFPGT-TDRIIMISG-TIDE 93 (291)
Q Consensus 34 ~~~~rilvp~~------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~------------~~~p~~-~er~v~I~G-~~~~ 93 (291)
.++-|+.||.+ .||+|||..|.|.|+|+++|||+|.|.-.. ...++. ++--+.|++ +.|.
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 56667777754 699999999999999999999999996521 112222 233477776 4678
Q ss_pred HHHHHHHHHHHHhh
Q 022837 94 ILRAVDLVIDKLLT 107 (291)
Q Consensus 94 v~~A~~~I~~~i~~ 107 (291)
|.+|++.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 89999998866665
No 46
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.71 E-value=9.2e-05 Score=62.43 Aligned_cols=103 Identities=19% Similarity=0.251 Sum_probs=70.8
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhcccccc
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQA 115 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~ 115 (291)
.+-+.+-.+.+|..||++|.+|+.|+++.|-+|.|-...+ . -...|...|....-..-..
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------d------~~~fI~nal~Pa~v~~V~~ 136 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------D------PAEFIKNALAPAEVLSVNI 136 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------C------HHHHHHHhcCcceEeEEEE
Confidence 4455666678999999999999999999998888854321 1 1122222221000000000
Q ss_pred CCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837 116 DDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (291)
Q Consensus 116 ~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 159 (291)
...+. ....+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus 137 ~~~d~-~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 137 KEDDG-HVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EeCCC-cEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 00011 27888899999999999999999999999999999976
No 47
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.70 E-value=5.6e-05 Score=60.86 Aligned_cols=104 Identities=14% Similarity=0.166 Sum_probs=74.5
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCC
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQT 201 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~ 201 (291)
..+.++|+...+|..||++|++|+.|++..|-+|.+-.-++ .+..+|...|.-..-.+-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~--------------------d~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSD--------------------DPEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCC--------------------CHHHHHHHHcCCCEEEEEE
Confidence 57889999999999999999999999999999988876211 1344555544332111100
Q ss_pred CCCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehcccc
Q 022837 202 MTVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLS 281 (291)
Q Consensus 202 ~~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~ 281 (291)
.. ....+....+.|+.+..|..||| +|.|++.++.-
T Consensus 92 I~------------------------------------------~~~~~~~~~V~V~~~d~g~aIGK--~G~ni~la~~L 127 (140)
T PRK08406 92 IK------------------------------------------KKNGDKVAYVEVAPEDKGIAIGK--NGKNIERAKDL 127 (140)
T ss_pred EE------------------------------------------ecCCcEEEEEEECccccchhhCC--CCHHHHHHHHH
Confidence 00 00011336788999999999999 99999999998
Q ss_pred ccceEEee
Q 022837 282 IYEEIRLN 289 (291)
Q Consensus 282 tga~i~~~ 289 (291)
+|-.+-|.
T Consensus 128 ~~~~~di~ 135 (140)
T PRK08406 128 AKRHFDID 135 (140)
T ss_pred hCCccCCe
Confidence 88877654
No 48
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.68 E-value=0.00052 Score=59.93 Aligned_cols=79 Identities=25% Similarity=0.282 Sum_probs=56.5
Q ss_pred CCceEEEEEecC------CccceeeccCChhHHHHHHhccceEEEecCCCCC--------------CCCCc---eEEEEE
Q 022837 119 GTKTKLRLIVPN------SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSY--------------YGLND---RLVTLT 175 (291)
Q Consensus 119 ~~~~~~~i~VP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~--------------~~~~e---r~V~I~ 175 (291)
....+.+++||- ++||+|+|..|.++|+|+++|||+|-|-...-.- ....+ -.|+..
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 345788999994 5999999999999999999999999997632110 01111 246667
Q ss_pred cCHHHH----HHHHHHHHHHHhcCcc
Q 022837 176 GTLDEQ----MRALELILLKLSEDTL 197 (291)
Q Consensus 176 G~~~~v----~~A~~~I~~~l~e~~~ 197 (291)
+++..+ ..|++.|.++|.-+.+
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P~~e 194 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVPDHE 194 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 775544 4588888888866544
No 49
>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=97.68 E-value=0.00017 Score=71.85 Aligned_cols=66 Identities=24% Similarity=0.299 Sum_probs=55.7
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHHh
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLL 106 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~ 106 (291)
.-+....|.||.+++|.|||+||.+||.|+++||++|.+.+ +-.|.|.+ ..+.+.+|+++|...+.
T Consensus 575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 34567889999999999999999999999999999999964 34577776 57889999999985554
No 50
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.61 E-value=0.0001 Score=74.24 Aligned_cols=91 Identities=19% Similarity=0.180 Sum_probs=68.6
Q ss_pred HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEE
Q 022837 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTL 174 (291)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I 174 (291)
.+|+..|++.|.+.+................+.||.+.++.+||.||.+||+|.++||+.|.+.. +..|.|
T Consensus 527 ~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------~G~v~i 597 (693)
T PRK11824 527 KEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------DGTVKI 597 (693)
T ss_pred HHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------CceEEE
Confidence 45566677777766543322222234456677789999999999999999999999999887742 467888
Q ss_pred EcC-HHHHHHHHHHHHHHHhc
Q 022837 175 TGT-LDEQMRALELILLKLSE 194 (291)
Q Consensus 175 ~G~-~~~v~~A~~~I~~~l~e 194 (291)
.+. .+.+++|+.+|..+..+
T Consensus 598 ~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 598 AATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred EcccHHHHHHHHHHHHHhccc
Confidence 885 88899999999988864
No 51
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.58 E-value=0.00011 Score=68.08 Aligned_cols=67 Identities=24% Similarity=0.340 Sum_probs=56.5
Q ss_pred CCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837 30 PTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (291)
Q Consensus 30 ~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~ 102 (291)
....++++.|.|-++.||.|||++|++||.||..|+++|++.+. ..+-.|+|.|...--.+|+..|-
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~------~~e~kv~ifg~~~m~~kaka~id 108 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC------DLEVKVTIFGINHMRKKAKASID 108 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc------CceeEEEEechHHHHHHHHhhHh
Confidence 45567889999999999999999999999999999999999763 35778999998776666666664
No 52
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.57 E-value=0.00021 Score=66.20 Aligned_cols=74 Identities=26% Similarity=0.359 Sum_probs=59.7
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCccc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLY 198 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~ 198 (291)
.....+-+-|-+++||.|||++|++||.||..|.++|++.+.+ .+-.|+|.|...--.+|...|...+..+..+
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~~~m~~kaka~id~~~~k~e~y 117 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGINHMRKKAKASIDRGQDKDERY 117 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEechHHHHHHHHhhHhhhhhhhhhc
Confidence 4456777888999999999999999999999999999998743 4678999999877777777776655544333
No 53
>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=97.47 E-value=0.00024 Score=71.47 Aligned_cols=64 Identities=19% Similarity=0.335 Sum_probs=52.6
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHH
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKL 105 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i 105 (291)
-+....+.||.+.+|.|||++|.+||.|+++|||+|.|.++ -.|.|.+ ..+.+.+|+++|....
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd---------G~V~i~~~~~~~~~~a~~~I~~~~ 613 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD---------GTVKIAASDGEAAEAAIKMIEGIT 613 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC---------eEEEEEECcHHHHHHHHHHHHhhh
Confidence 45678899999999999999999999999999999999652 3355554 5778899988887543
No 54
>PRK00106 hypothetical protein; Provisional
Probab=97.39 E-value=0.001 Score=64.70 Aligned_cols=67 Identities=19% Similarity=0.251 Sum_probs=51.1
Q ss_pred CceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 022837 120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE 194 (291)
Q Consensus 120 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e 194 (291)
......+.+|+ ++-|+||||.|.||+.+...||+.+.|.+ +...|+|+|. |-.-+-|+..+..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34566677887 56799999999999999999999999976 4467889994 55555566555555543
No 55
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.38 E-value=0.00028 Score=63.33 Aligned_cols=71 Identities=20% Similarity=0.333 Sum_probs=58.8
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE 108 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~ 108 (291)
.+..-++|++...|.|||++|.|.++|+++|+++|.++..++ ..+.++.+.++.++|.+|.+.|...|...
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~----n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT----NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC----CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 467778999999999999999999999999999999998543 24455555668899999999998666544
No 56
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.37 E-value=0.00097 Score=64.94 Aligned_cols=67 Identities=21% Similarity=0.221 Sum_probs=50.8
Q ss_pred CceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhc
Q 022837 120 TKTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSE 194 (291)
Q Consensus 120 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e 194 (291)
......+.+|+ ++-|+||||.|.|||.++..||+.|.|.+ +...|+|+|. |-.-+-|+..+..++.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34556677887 56699999999999999999999999976 3457889994 55555566655555543
No 57
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.37 E-value=0.0013 Score=57.41 Aligned_cols=45 Identities=16% Similarity=0.377 Sum_probs=38.8
Q ss_pred CCCCCcEEEEEEeccc------ccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 29 DPTEKPTYIRFLVSNP------LAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 29 ~~~~~~~~~rilvp~~------~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
+...-.++.||+||.+ .||+|+|..|.++|+|+++|||+|.|.-.
T Consensus 86 ~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 86 SGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred cCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 3445567899999976 69999999999999999999999999653
No 58
>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=97.36 E-value=0.00037 Score=47.79 Aligned_cols=37 Identities=27% Similarity=0.451 Sum_probs=34.5
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEE
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v 70 (291)
...+.+.|+.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3679999999999999999999999999999988876
No 59
>PRK12704 phosphodiesterase; Provisional
Probab=97.35 E-value=0.0011 Score=64.68 Aligned_cols=65 Identities=22% Similarity=0.200 Sum_probs=49.1
Q ss_pred ceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHh
Q 022837 121 KTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLS 193 (291)
Q Consensus 121 ~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~ 193 (291)
.....+.+|+ ++-|+||||.|.|||.++..||+.|.|.+ +...|.|+|. +-.-+.|...+..++.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHHh
Confidence 3455667887 66799999999999999999999999976 3467889994 5444455555555444
No 60
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.30 E-value=0.00064 Score=56.99 Aligned_cols=53 Identities=21% Similarity=0.337 Sum_probs=47.1
Q ss_pred ccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837 45 LAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT 107 (291)
Q Consensus 45 ~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~ 107 (291)
..|+|||++|.|-+.|++-|+|.|.|.. ..|.|-|.++++..|++.|..++..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcC
Confidence 4699999999999999999999999953 5699999999999999999866543
No 61
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.19 E-value=0.028 Score=48.27 Aligned_cols=131 Identities=13% Similarity=0.105 Sum_probs=93.6
Q ss_pred EEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCC
Q 022837 38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADD 117 (291)
Q Consensus 38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~ 117 (291)
.+.++....-++...+|..++.|-...|++|.+.. .+..|.|+|+...+..+...|.+.+..-
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i--------- 91 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNI--------- 91 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhc---------
Confidence 34445778889999999999999888899999965 3468999999998888888887555332
Q ss_pred CCCceEEEEEecCCccceee----ccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEE-----cCHHHHHHHHHHH
Q 022837 118 VGTKTKLRLIVPNSSCGSII----GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLT-----GTLDEQMRALELI 188 (291)
Q Consensus 118 ~~~~~~~~i~VP~~~vg~II----Gk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~-----G~~~~v~~A~~~I 188 (291)
.+..+.++.-.--..- -.....++.|++.|++.|...++ +..+.|+ -....++.|+.++
T Consensus 92 ----~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~--------~~~~~i~~~~~~~~~~~~~~a~RlL 159 (210)
T PF14611_consen 92 ----RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD--------GNKLKISWLASPENEKRADRAKRLL 159 (210)
T ss_pred ----EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC--------CCeEEEEEEeeccccchHHHHHHHH
Confidence 3444444432211111 12356799999999999998763 2334444 4678899999999
Q ss_pred HHHHhcCcc
Q 022837 189 LLKLSEDTL 197 (291)
Q Consensus 189 ~~~l~e~~~ 197 (291)
...+..++.
T Consensus 160 ~~a~~~~~~ 168 (210)
T PF14611_consen 160 LWALDYNPH 168 (210)
T ss_pred HHhccCCcc
Confidence 998864444
No 62
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=97.12 E-value=0.0011 Score=61.14 Aligned_cols=95 Identities=20% Similarity=0.311 Sum_probs=66.0
Q ss_pred cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837 44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (291)
Q Consensus 44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (291)
+-+|+.||++|.+|+.|.++. |-+|.|-..++ + + ..+|...|.-..-..-...+ ....
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d--------~------~~fi~nal~Pa~v~~v~i~~-~~~~ 301 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSD------D--------P------AEFIANALSPAKVISVEVLD-EDKH 301 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCC------C--------H------HHHHHHhcCCceEEEEEEEc-CCCc
Confidence 358999999999999999998 88888865332 1 1 11222111110000000001 1225
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 159 (291)
...+.||.+..+..|||+|.|++-...-||.+|.|..
T Consensus 302 ~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 302 SAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 7899999999999999999999999999999999976
No 63
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.11 E-value=0.0011 Score=61.37 Aligned_cols=95 Identities=17% Similarity=0.182 Sum_probs=66.6
Q ss_pred cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837 44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (291)
Q Consensus 44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (291)
+-+|..||++|.+|+.|.++. |-+|.|-..++ + -..+|...|.-..-.. .... ....
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~------D--------------~~~fI~Nal~Pa~V~~-V~i~-~~~~ 308 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSN------V--------------PEIFIARALAPAIISS-VKIE-EEEK 308 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCC------C--------------HHHHHHHhCCCceeeE-EEEc-CCCc
Confidence 458999999999999999998 88888865332 1 1122222221110000 0000 2235
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
...+.||.+..+..|||+|.|++-...-||.+|.|..-
T Consensus 309 ~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 309 KAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred EEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 78889999999999999999999999999999999873
No 64
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.10 E-value=0.00099 Score=61.85 Aligned_cols=96 Identities=23% Similarity=0.329 Sum_probs=67.2
Q ss_pred cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837 44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (291)
Q Consensus 44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (291)
+-+|+.||++|.+|+.|.++. |-+|.|-..++ + ...+|...|.-..-..-...+ ....
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~------d--------------~~~fi~nal~Pa~v~~v~i~~-~~~~ 303 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSE------D--------------PAEFVANALSPAKVVSVEVDD-EEEK 303 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCC------C--------------HHHHHHHhCCCceEEEEEEEc-CCCc
Confidence 358999999999999999998 88888865432 1 112222222111000000001 2235
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
...+.||.+..+..|||+|.|++-...-||.+|.|...
T Consensus 304 ~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 304 AARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 78899999999999999999999999999999999873
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.06 E-value=0.00077 Score=60.58 Aligned_cols=72 Identities=24% Similarity=0.293 Sum_probs=59.5
Q ss_pred ceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCc
Q 022837 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDT 196 (291)
Q Consensus 121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~ 196 (291)
.....+.|+..+.|.|||++|.+.++|+++|+++|.++.... ..+.++.+.+..++|.+|.+.|..+|.+..
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT----NKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC----CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 356778899999999999999999999999999999987321 234455555679999999999999988754
No 66
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=97.05 E-value=0.0011 Score=45.39 Aligned_cols=36 Identities=28% Similarity=0.452 Sum_probs=33.8
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEE
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKI 157 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 157 (291)
....+.|+.+..|..|||+|.+|+.++..+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 688999999999999999999999999999988876
No 67
>PRK00468 hypothetical protein; Provisional
Probab=97.03 E-value=0.00077 Score=48.16 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=30.8
Q ss_pred CCCcEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
.++.+.+++.|..+.+|+||||+|.+|+.||.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 44568999999999999999999999999998644
No 68
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.90 E-value=0.0021 Score=56.43 Aligned_cols=65 Identities=17% Similarity=0.231 Sum_probs=55.2
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCc
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLSEDT 196 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~e~~ 196 (291)
-+.+.||..+++++||++|.+|+.|.+.++++|.+-. +..|.|.++ .+.+.+|..+|..+-++..
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 3568899999999999999999999999999999864 367889888 5588889999988766643
No 69
>PRK02821 hypothetical protein; Provisional
Probab=96.86 E-value=0.0013 Score=47.17 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=31.2
Q ss_pred CCCcEEEEEEecccccceeeccCChhHHHHHHHhCC
Q 022837 31 TEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGA 66 (291)
Q Consensus 31 ~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga 66 (291)
.++.+.+++.|..+.+|+||||+|.+|+.||.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345588999999999999999999999999987654
No 70
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.86 E-value=0.0015 Score=61.51 Aligned_cols=95 Identities=23% Similarity=0.275 Sum_probs=65.8
Q ss_pred cccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCce
Q 022837 44 PLAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKT 122 (291)
Q Consensus 44 ~~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 122 (291)
+-+|..||++|.+|+.|.++. |-+|.|-.-++ + + ..+|...|.-..-..-...+ ....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~------D--------p------~~fI~NaLsPA~V~~V~i~~-~~~k 335 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSP------D--------P------ATYIANALSPARVDEVRLVD-PEGR 335 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCC------C--------H------HHHHHHhcCCceeeEEEEEc-CCCc
Confidence 458999999999999999999 88888865332 1 1 12222222111000000001 1224
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 159 (291)
...+.||.+..+..|||+|.|++-...-||.+|.|..
T Consensus 336 ~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 HAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 6789999999999999999999999999999999975
No 71
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.83 E-value=0.0023 Score=53.90 Aligned_cols=41 Identities=29% Similarity=0.440 Sum_probs=35.8
Q ss_pred CCceEEEEEec------CCccceeeccCChhHHHHHHhccceEEEec
Q 022837 119 GTKTKLRLIVP------NSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (291)
Q Consensus 119 ~~~~~~~i~VP------~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 159 (291)
....+-++.|| .++||.|||..|.|.|++++.|+|+|.|-.
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 34467778887 679999999999999999999999999976
No 72
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.72 E-value=0.0022 Score=65.56 Aligned_cols=66 Identities=15% Similarity=0.315 Sum_probs=54.9
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhCCc-EEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHHh
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGAR-IQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLL 106 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~-I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~ 106 (291)
.-+....|.||.++++.|||.||.+||.|.++||++ |++.+ +-.|.|.+ ..+.+.+|+++|.+.+.
T Consensus 682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 345678899999999999999999999999999999 99964 24466666 57889999999876554
No 73
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.72 E-value=0.002 Score=45.94 Aligned_cols=34 Identities=35% Similarity=0.432 Sum_probs=30.6
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
++.+.+++.+..+..|.||||+|.+|+.||.--.
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~ 60 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLS 60 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHHH
Confidence 6678999999999999999999999999997543
No 74
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.61 E-value=0.0021 Score=61.71 Aligned_cols=94 Identities=21% Similarity=0.298 Sum_probs=65.9
Q ss_pred ccceeeccCChhHHHHHHHh-CCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceE
Q 022837 45 LAGAVIGKGGSTINDFQSQS-GARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTK 123 (291)
Q Consensus 45 ~vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~ 123 (291)
-+|+.||++|.+|+.|.++. |-+|.|-.-++ + + ..+|...|.-..-.. -..+ .....
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~------d--------~------~~fi~nal~pa~v~~-v~~~-~~~~~ 303 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSD------D--------P------AQFIINALSPAEVSS-VVVD-EDEHS 303 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCC------C--------H------HHHHHHhCCCCEEEE-EEEe-CCCCE
Confidence 48999999999999999998 78888865332 1 1 122222221110000 0000 11248
Q ss_pred EEEEecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
..+.||.+..+..|||+|.|++...+.||.+|.|...
T Consensus 304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 8899999999999999999999999999999999763
No 75
>PRK12705 hypothetical protein; Provisional
Probab=96.60 E-value=0.0053 Score=59.43 Aligned_cols=65 Identities=18% Similarity=0.188 Sum_probs=44.4
Q ss_pred ceEEEEEecC-CccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHh
Q 022837 121 KTKLRLIVPN-SSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT-LDEQMRALELILLKLS 193 (291)
Q Consensus 121 ~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~-~~~v~~A~~~I~~~l~ 193 (291)
.....+.+|+ ++-|+||||.|.|||.++..||+.|.|.+ ..+.|+|++. +..-+.|...+..++.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD--------TPEAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC--------CccchhhcccCccchHHHHHHHHHHHh
Confidence 3455566776 56699999999999999999999999976 2344666664 3333334444444433
No 76
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.55 E-value=0.0037 Score=61.54 Aligned_cols=62 Identities=18% Similarity=0.284 Sum_probs=51.8
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCH-HHHHHHHHHHHHHH
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTI-DEILRAVDLVIDKL 105 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~-~~v~~A~~~I~~~i 105 (291)
-...+.|+.+.++.+||++|.+|++|.++||++|++.++ -.|.|.++. +.+.+|++.|....
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd---------Gtv~i~~s~~~~~~~ak~~I~~i~ 614 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD---------GTVKIAASDGESAKKAKERIEAIT 614 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC---------CcEEEEecchHHHHHHHHHHHHHH
Confidence 456788899999999999999999999999999999743 347777765 67888888887555
No 77
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.54 E-value=0.0069 Score=58.22 Aligned_cols=93 Identities=16% Similarity=0.168 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEE
Q 022837 94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVT 173 (291)
Q Consensus 94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~ 173 (291)
...|+..|++.+.+.+............+...+.|+.+....+||.+|...|+|..+||+.-++ ++.+++
T Consensus 569 a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----------De~t~~ 638 (760)
T KOG1067|consen 569 AREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----------DEGTFS 638 (760)
T ss_pred hhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee----------cCceEE
Confidence 3456677888787776544333344566788899999999999999999999999999954444 346788
Q ss_pred EEcC-HHHHHHHHHHHHHHHhcCc
Q 022837 174 LTGT-LDEQMRALELILLKLSEDT 196 (291)
Q Consensus 174 I~G~-~~~v~~A~~~I~~~l~e~~ 196 (291)
|.-. +.+.++|++.|..++..+.
T Consensus 639 i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 639 IFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred EEecCHHHHHHHHHHHHHHhcCcc
Confidence 7775 7888999999999887743
No 78
>PRK01064 hypothetical protein; Provisional
Probab=96.50 E-value=0.0036 Score=45.06 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=30.5
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
++.+.+++.|..+..|.+|||+|.+|+.||.-..
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 4668999999999999999999999999998643
No 79
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.43 E-value=0.0086 Score=52.51 Aligned_cols=62 Identities=26% Similarity=0.324 Sum_probs=50.4
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecC-HHHHHHHHHHHHHHHhhh
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGT-IDEILRAVDLVIDKLLTE 108 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~-~~~v~~A~~~I~~~i~~~ 108 (291)
+.+.||..+++.+||++|.+|+.|.++|+++|.+-.+ -.|.|.+. .+++..|+.+|. .+.++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N---------G~VwI~~~~~~~~~~a~~~I~-~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN---------GRIWIKGPDEEDEEIAIEAIK-KIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC---------cEEEEeeCCHHHHHHHHHHHH-HHHhh
Confidence 5588999999999999999999999999999999542 34777775 558888888886 45444
No 80
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=96.41 E-value=0.0038 Score=50.24 Aligned_cols=103 Identities=15% Similarity=0.150 Sum_probs=69.1
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccCCCC
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYSQTM 202 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~ 202 (291)
..-++|....+|..||++|++|+.|++..|-+|.+-.-+ .++ .++|...|.-..-. ..
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys--------------~D~------~~fI~N~l~PA~V~--~V 91 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS--------------ENL------EEFVANKLAPAEVK--NV 91 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC--------------CCH------HHHHHHcCCCceEE--EE
Confidence 777889999999999999999999999999888886521 111 12222222110000 00
Q ss_pred CCCccCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCeEEEeecCCCcceeEEeecCccceehccccc
Q 022837 203 TVPYTYAGVFFSGFHGMPYGAVPPPVPAVPHNTAAHYGPNMGGRKFQNNKVLLPWPLNPVGMLLIILIAQPIICHFSLSI 282 (291)
Q Consensus 203 ~~~~~~~g~~~~~~~g~p~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iP~~~vG~iIG~~~gg~~ik~~~~~t 282 (291)
. .. .........+.||.+..|..||| +|.||+-.++=+
T Consensus 92 ~--i~--------------------------------------~~~~~~~a~V~V~~~d~~~AIGk--~G~Ni~la~~l~ 129 (141)
T TIGR01952 92 T--VS--------------------------------------EFNGKKVAYVEVHPRDKGIAIGK--GGKNIERAKELA 129 (141)
T ss_pred E--EE--------------------------------------cCCCCEEEEEEEChhhhhhhhCC--CchhHHHHHHHh
Confidence 0 00 00011347789999999999999 999999998888
Q ss_pred cceEEee
Q 022837 283 YEEIRLN 289 (291)
Q Consensus 283 ga~i~~~ 289 (291)
|-.+-|.
T Consensus 130 ~~~~dI~ 136 (141)
T TIGR01952 130 KRHHDID 136 (141)
T ss_pred cCccCCe
Confidence 8776553
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.33 E-value=0.011 Score=49.93 Aligned_cols=40 Identities=25% Similarity=0.390 Sum_probs=33.9
Q ss_pred cEEEEEEecc------cccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 34 PTYIRFLVSN------PLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 34 ~~~~rilvp~------~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
.+.-++.||. +.||+|||..|.|+|+|+..|+|+|-|...
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3566677764 479999999999999999999999999653
No 82
>PRK02821 hypothetical protein; Provisional
Probab=96.33 E-value=0.0071 Score=43.38 Aligned_cols=35 Identities=23% Similarity=0.320 Sum_probs=29.7
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhccc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQA 153 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa 153 (291)
.....+.+.+..+.+|+||||+|.+|+.|+.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 34478899999999999999999999999876443
No 83
>PRK00468 hypothetical protein; Provisional
Probab=96.32 E-value=0.0049 Score=44.05 Aligned_cols=33 Identities=27% Similarity=0.343 Sum_probs=29.0
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
......++.+..+.+|+||||+|.+|+.|+.--
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 445788999999999999999999999998754
No 84
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.92 E-value=0.0099 Score=42.41 Aligned_cols=33 Identities=27% Similarity=0.391 Sum_probs=29.2
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
......+|.+.....|+||||+|.+|+.|+.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 456789999999999999999999999998653
No 85
>PRK12704 phosphodiesterase; Provisional
Probab=95.63 E-value=0.032 Score=54.57 Aligned_cols=49 Identities=22% Similarity=0.480 Sum_probs=39.2
Q ss_pred CcEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837 33 KPTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89 (291)
Q Consensus 33 ~~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G 89 (291)
..++--+.+|+ +.-|+||||.|.||+.++.-||+.|-|.+ +..+|.|+|
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~ 257 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSG 257 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEec
Confidence 34445566777 58999999999999999999999999964 234577888
No 86
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.55 E-value=0.015 Score=58.95 Aligned_cols=63 Identities=21% Similarity=0.313 Sum_probs=50.2
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHH
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKL 105 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i 105 (291)
+....+.|+.+.++.+||.+|.+||+|.++||++|.+.++ -.|.|.+ ..+.+.+|+++|....
T Consensus 553 p~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d~---------G~v~i~~~~~~~~~~a~~~I~~~~ 616 (693)
T PRK11824 553 PRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIEDD---------GTVKIAATDGEAAEAAKERIEGIT 616 (693)
T ss_pred chheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCCC---------ceEEEEcccHHHHHHHHHHHHHhc
Confidence 3445666799999999999999999999999999998542 3366666 5678889988887544
No 87
>PRK01064 hypothetical protein; Provisional
Probab=95.50 E-value=0.019 Score=41.32 Aligned_cols=33 Identities=33% Similarity=0.391 Sum_probs=29.0
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
...+.+++.+..+..|++|||+|.+|+.|+.-.
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 455788999999999999999999999998753
No 88
>PRK00106 hypothetical protein; Provisional
Probab=95.48 E-value=0.046 Score=53.36 Aligned_cols=49 Identities=20% Similarity=0.511 Sum_probs=39.5
Q ss_pred CcEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837 33 KPTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89 (291)
Q Consensus 33 ~~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G 89 (291)
..++--+.+|+ +.-|+||||.|.||+.++.-||+.+-|.+. ...|+|+|
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--------p~~v~lS~ 272 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT--------PEVVVLSG 272 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC--------CCeEEEeC
Confidence 44556677787 589999999999999999999999999642 23466777
No 89
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.48 E-value=0.043 Score=53.61 Aligned_cols=49 Identities=20% Similarity=0.473 Sum_probs=39.2
Q ss_pred CcEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec
Q 022837 33 KPTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG 89 (291)
Q Consensus 33 ~~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G 89 (291)
..++--+.+|+ +.-|+||||.|.||+.++.-||+.|-|.+. ...|+|++
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt--------p~~v~ls~ 251 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT--------PEAVILSG 251 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC--------CCeEEecC
Confidence 44555677787 589999999999999999999999999642 23466777
No 90
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.01 E-value=0.011 Score=41.93 Aligned_cols=37 Identities=32% Similarity=0.352 Sum_probs=30.6
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcE
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARI 68 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I 68 (291)
.+...+.+-+..+..|.||||+|.+++.||.-.+.-+
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 3456688888999999999999999999998766443
No 91
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.48 E-value=0.036 Score=57.51 Aligned_cols=71 Identities=17% Similarity=0.176 Sum_probs=60.7
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
...++.+|.....+|||++|.+|+.++.-|||.|.+.+-.. .+..||.+.+.|.++.+.-|...|.-.+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~--~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP--DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC--ccchhhhcccCCCChhhhhhhccccceeec
Confidence 45678899999999999999999999999999999987211 234789999999999999999888876654
No 92
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.42 E-value=0.45 Score=40.76 Aligned_cols=66 Identities=18% Similarity=0.170 Sum_probs=57.1
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSED 195 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~ 195 (291)
..+.+.++....-.|...+|..++.|....||+|.+.. .+..|.|+|+...+..+...|.+.+..-
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 35556667888899999999999999888899999987 4579999999999999999999988764
No 93
>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=94.37 E-value=0.079 Score=36.19 Aligned_cols=35 Identities=29% Similarity=0.337 Sum_probs=29.1
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcE
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARI 68 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I 68 (291)
...+.+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45666777776789999999999999999998554
No 94
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=94.12 E-value=0.17 Score=40.59 Aligned_cols=95 Identities=17% Similarity=0.261 Sum_probs=65.1
Q ss_pred eeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEEEe
Q 022837 49 VIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIV 128 (291)
Q Consensus 49 IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~V 128 (291)
.+=.+|..|++|-++..-+|.|..+... .- .=..|.+.|.+.+-++..- .+-.-+..+-++.|
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~dps~-----------l~---~~e~A~~~I~~ivP~ea~i---~di~Fd~~tGEV~I 82 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPDPSV-----------LK---PPEEAIKIILEIVPEEAGI---TDIYFDDDTGEVII 82 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCChhh-----------cC---CHHHHHHHHHHhCCCccCc---eeeEecCCCcEEEE
Confidence 4446788999999999988888654211 11 1145878887655333110 00011224667788
Q ss_pred cCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 129 PNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 129 P~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
-...-|.+||++|.++++|..+||-.-.+...
T Consensus 83 eaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 83 EAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 88888999999999999999999988888763
No 95
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=93.81 E-value=0.051 Score=38.17 Aligned_cols=37 Identities=30% Similarity=0.444 Sum_probs=30.2
Q ss_pred EEEEecccc-----cceeeccCChhHHHHHHHh-CCcEEEcCC
Q 022837 37 IRFLVSNPL-----AGAVIGKGGSTINDFQSQS-GARIQLSRS 73 (291)
Q Consensus 37 ~rilvp~~~-----vG~IIGk~G~~Ik~I~~~t-ga~I~v~~~ 73 (291)
.++.|-+.. +|..||++|.+|+.|.++. |-+|+|-..
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 567777777 9999999999999999999 899988654
No 96
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=93.69 E-value=0.077 Score=50.36 Aligned_cols=67 Identities=19% Similarity=0.232 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCC
Q 022837 94 ILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD 161 (291)
Q Consensus 94 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~ 161 (291)
...|.+.|...+.+.++.. ....-.......+.||..+++.+|||+|.+|++|+++.|.+|.|...+
T Consensus 459 ~~~a~~~i~~~i~r~~p~~-~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 459 LKLAEEEIEREIKRYLPGD-VEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred hHHHHHHHHHHHHHhCCCC-ceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 4456666665555554421 111112234677889999999999999999999999999999998743
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.54 E-value=0.037 Score=39.17 Aligned_cols=35 Identities=20% Similarity=0.324 Sum_probs=29.8
Q ss_pred CCceEEEEEecCCccceeeccCChhHHHHHHhccc
Q 022837 119 GTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQA 153 (291)
Q Consensus 119 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa 153 (291)
.......+.+..+..|.||||.|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 34568888899999999999999999999976554
No 98
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=93.43 E-value=0.034 Score=46.71 Aligned_cols=56 Identities=30% Similarity=0.381 Sum_probs=49.0
Q ss_pred ccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhh
Q 022837 43 NPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTE 108 (291)
Q Consensus 43 ~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~ 108 (291)
+..+|+|+||+|.+--.|++.|.++|.+.. ..|.|-|..+|+.-|...|...|.-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHHHHHhhHhhhccC
Confidence 457899999999999999999999999953 55999999999999999998776543
No 99
>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=93.10 E-value=0.19 Score=34.19 Aligned_cols=34 Identities=24% Similarity=0.456 Sum_probs=27.6
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceE
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI 155 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I 155 (291)
....+.+.....|.+||++|.+++.++..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 5556666666789999999999999999987544
No 100
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=93.08 E-value=0.063 Score=45.12 Aligned_cols=150 Identities=11% Similarity=0.047 Sum_probs=88.4
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccc--
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAE-- 112 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~-- 112 (291)
-+-++.||....--+=-.==....-|-+..+..|.+.-... ..+-|.+.-+-.+.+++++.+.|...+.-..-.+
T Consensus 74 e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r---~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAi 150 (252)
T KOG3273|consen 74 ETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKAR---SVELRTCKDTEDPSALQKGADFVRAFILGFDIDDAI 150 (252)
T ss_pred ceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccc---eeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHH
Confidence 34567777765433211111112345566666666632211 1122333334456788888777765443220000
Q ss_pred -----cc-cC---CCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHH
Q 022837 113 -----DQ-AD---DVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183 (291)
Q Consensus 113 -----~~-~~---~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~ 183 (291)
++ .. +-.+..+++=.=-...+|+|+||+|.+--.|++.|.++|.+.. ..|-|-|..+++.-
T Consensus 151 ALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niri 220 (252)
T KOG3273|consen 151 ALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRI 220 (252)
T ss_pred HHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHH
Confidence 00 00 0011112222222456899999999999999999999999864 57999999999999
Q ss_pred HHHHHHHHHhcCcc
Q 022837 184 ALELILLKLSEDTL 197 (291)
Q Consensus 184 A~~~I~~~l~e~~~ 197 (291)
|+..|+.++-.+|.
T Consensus 221 AR~avcsLIlGspp 234 (252)
T KOG3273|consen 221 ARDAVCSLILGSPP 234 (252)
T ss_pred HHHhhHhhhccCCc
Confidence 99999999987654
No 101
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=93.08 E-value=0.21 Score=43.49 Aligned_cols=55 Identities=22% Similarity=0.317 Sum_probs=43.7
Q ss_pred EEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHH-HHHHHHHHHH
Q 022837 39 FLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTID-EILRAVDLVI 102 (291)
Q Consensus 39 ilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~-~v~~A~~~I~ 102 (291)
+.|+...|.++||++|+.++.|.++|+|+|-|-.+. .|.|.+..+ ...-|...|.
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~NG---------~IWV~~~~~~~e~~~~~aI~ 205 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQNG---------RIWVDGENESLEELAIEAIR 205 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecCC---------EEEecCCCcchHHHHHHHHH
Confidence 688999999999999999999999999999996533 377777665 3444545554
No 102
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=92.93 E-value=0.2 Score=44.31 Aligned_cols=51 Identities=16% Similarity=0.221 Sum_probs=45.9
Q ss_pred ceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 134 GSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 134 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
-+|||.+|.|+|.|+--|.|.|-|.. .+|.+.|....+..+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG----------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG----------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 38999999999999999999999975 4799999999999999988887765
No 103
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.88 E-value=0.087 Score=54.82 Aligned_cols=69 Identities=20% Similarity=0.131 Sum_probs=58.3
Q ss_pred CCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837 32 EKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (291)
Q Consensus 32 ~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~ 102 (291)
-.....++.+|.....+|||++|.+|..++..||+.|.|.+-.. .+..||.+.+.|.++.+.-|...|.
T Consensus 1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~--~Nqaers~~~kg~p~~~r~a~~~I~ 1405 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP--DNQAERSKAPKGRPPSQRVATSPIG 1405 (2131)
T ss_pred CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC--ccchhhhcccCCCChhhhhhhcccc
Confidence 34457789999999999999999999999999999999976221 1346899999999999998887775
No 104
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=92.80 E-value=0.13 Score=36.86 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=28.7
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEE
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v 70 (291)
.+.+-+..+..|.+|||+|.++..||--.+.-++-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 35666777889999999999999999987765554
No 105
>PRK13764 ATPase; Provisional
Probab=92.60 E-value=0.14 Score=50.80 Aligned_cols=66 Identities=23% Similarity=0.238 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCC
Q 022837 95 LRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLD 161 (291)
Q Consensus 95 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~ 161 (291)
..|.+.|.+.+.+..... ...+........+.||...++.+|||+|.+|++|.++.|.+|.|.+.+
T Consensus 455 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 455 RLAEKEIEREIKRYLPGP-VEVEVVSDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred HHHHHHHHHHHHHhcCCc-eEEEEecCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 445556655555443111 111112345788899999999999999999999999999999998744
No 106
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=92.41 E-value=0.21 Score=47.87 Aligned_cols=97 Identities=20% Similarity=0.261 Sum_probs=70.2
Q ss_pred ceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEE
Q 022837 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRL 126 (291)
Q Consensus 47 G~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i 126 (291)
..++-+.|..||+|-++..-+|.+..+...+ ..-+.|.+.|++.+-++..-. +..-+..+-++
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dPsvl--------------~~~e~A~~~I~eivP~ea~i~---~i~Fd~~tGEV 103 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDPSVL--------------KPPEEARKIILEIVPEEAGIT---DIYFDDDTGEV 103 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCchhc--------------CCHHHHHHHHHHhCccccCce---eEEecCCCceE
Confidence 4567789999999999999999997643211 123568888886664441111 11122346778
Q ss_pred EecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 127 IVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 127 ~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
+|-...=|.+|||+|++.++|..+||-.-.|.+.
T Consensus 104 iIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 104 IIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred EEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 8889999999999999999999999987777763
No 107
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.02 E-value=0.12 Score=36.27 Aligned_cols=37 Identities=24% Similarity=0.476 Sum_probs=30.0
Q ss_pred EEEEEecCCc-----cceeeccCChhHHHHHHhc-cceEEEec
Q 022837 123 KLRLIVPNSS-----CGSIIGKAGATIKSFMDDS-QAVIKISR 159 (291)
Q Consensus 123 ~~~i~VP~~~-----vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~ 159 (291)
..++.|-... +|..||++|.+||.|+++. |-+|++-.
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 4566666666 8999999999999999999 99999876
No 108
>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=92.01 E-value=0.086 Score=37.69 Aligned_cols=35 Identities=26% Similarity=0.449 Sum_probs=30.1
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEE
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQ 69 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~ 69 (291)
-.+.+.+...+.|.|||++|++|++|++..+-.+.
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 34678889999999999999999999998876664
No 109
>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=91.95 E-value=0.21 Score=35.75 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=27.6
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceE
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI 155 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I 155 (291)
....+.+..+..|.||||.|++++.||--...-+
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 3566778889999999999999999997765433
No 110
>PRK12705 hypothetical protein; Provisional
Probab=91.78 E-value=0.28 Score=47.75 Aligned_cols=40 Identities=18% Similarity=0.439 Sum_probs=33.1
Q ss_pred cEEEEEEecc-cccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 34 PTYIRFLVSN-PLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 34 ~~~~rilvp~-~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
.++--+.+|+ +.-|+||||.|.||+.++..||+.|-|.+.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 3444556666 589999999999999999999999999753
No 111
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=90.61 E-value=0.26 Score=41.70 Aligned_cols=37 Identities=22% Similarity=0.294 Sum_probs=35.2
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR 72 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~ 72 (291)
.+.+.||.++.+.+|||+|.+++.+.+-||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7889999999999999999999999999999999965
No 112
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=90.58 E-value=0.2 Score=47.67 Aligned_cols=39 Identities=26% Similarity=0.406 Sum_probs=35.5
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCC
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH 74 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~ 74 (291)
...+.||..+++.+|||+|.+|++|++..|.+|.|....
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 366889999999999999999999999999999997654
No 113
>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=90.57 E-value=0.11 Score=37.07 Aligned_cols=35 Identities=23% Similarity=0.495 Sum_probs=29.9
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEE
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIK 156 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~ 156 (291)
....+.+...+-|.|||++|++|++|....+-.+.
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 46788899999999999999999999887765553
No 114
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.56 E-value=0.83 Score=39.80 Aligned_cols=59 Identities=19% Similarity=0.261 Sum_probs=45.5
Q ss_pred EEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHH-HHHHHHHHHHH
Q 022837 124 LRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDE-QMRALELILLK 191 (291)
Q Consensus 124 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~-v~~A~~~I~~~ 191 (291)
.-+.|+...+.++||++|+.++-|.+.++|+|-+-.+ ..|=|.|..+. ...|...|..+
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 5578999999999999999999999999999999752 45777777653 44444444443
No 115
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=90.28 E-value=0.51 Score=41.81 Aligned_cols=51 Identities=18% Similarity=0.274 Sum_probs=44.1
Q ss_pred ceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhh
Q 022837 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLT 107 (291)
Q Consensus 47 G~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~ 107 (291)
-++||.+|.|+|.|+--|.|.|-|.. ..|.+.|....+..+.+.+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG----------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG----------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 46999999999999999999999953 4588999999999998888877754
No 116
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=90.02 E-value=0.46 Score=44.30 Aligned_cols=40 Identities=20% Similarity=0.172 Sum_probs=36.8
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCC
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSH 74 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~ 74 (291)
-.+.+.||.++.++.|||+|.|++-..+-||.+|.|..-.
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 4788999999999999999999999999999999997643
No 117
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=89.82 E-value=0.55 Score=45.66 Aligned_cols=99 Identities=19% Similarity=0.268 Sum_probs=68.6
Q ss_pred CCCCCcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEec-CHHHHHHHHHHHHHHHhh
Q 022837 29 DPTEKPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISG-TIDEILRAVDLVIDKLLT 107 (291)
Q Consensus 29 ~~~~~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~~ 107 (291)
+....++...+.|+.+....+||.+|-..|+|+.+||+.-.+. +-.+.|.. ++...++|++.|...+..
T Consensus 591 ~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----------e~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 591 DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----------EGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------CceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 3445678889999999999999999999999999999666663 23455554 577889999998765544
Q ss_pred hhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837 108 ELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (291)
Q Consensus 108 ~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 159 (291)
+-.++ -..|.|- -.+|++|+ ++|+-+.+.+
T Consensus 661 ~~~~~------------------l~~g~vy---~~tIt~~r-d~G~~V~l~p 690 (760)
T KOG1067|consen 661 DQVQD------------------LEFGGVY---TATITEIR-DTGVMVELYP 690 (760)
T ss_pred ccccc------------------eEeeeEE---EEEEeeec-ccceEEEecC
Confidence 31111 1112111 23466766 4889888887
No 118
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=89.81 E-value=0.51 Score=38.98 Aligned_cols=36 Identities=22% Similarity=0.440 Sum_probs=31.5
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
+-|+|.... |..|||+|.+++++++..|-+|.+-..
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 456777777 999999999999999999999999754
No 119
>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=89.71 E-value=0.58 Score=46.98 Aligned_cols=97 Identities=15% Similarity=0.201 Sum_probs=67.9
Q ss_pred ceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEE
Q 022837 47 GAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRL 126 (291)
Q Consensus 47 G~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i 126 (291)
...+=.+|..||+|-++..-+|.|..+.. +.-. -+.|.+.|.+.+-++.. -.+-.-+..+-++
T Consensus 35 ~~~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------~~~~---~~~~~~~i~~~~~~~~~---~~~~~f~~~~~~v 97 (630)
T TIGR03675 35 PELFAKDDDLVKELAKKLRKRIVIRPDPS-----------VLLP---PEEAIEKIKEIVPEEAG---ITDIYFDDVTGEV 97 (630)
T ss_pred HHHhccchHHHHHHHHHhhceEEEecChh-----------hcCC---HHHHHHHHHHhCCCcCC---ceeEEecCCCceE
Confidence 34566788999999999999999965432 1111 24577777755533311 0011112346778
Q ss_pred EecCCccceeeccCChhHHHHHHhccceEEEecC
Q 022837 127 IVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRL 160 (291)
Q Consensus 127 ~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 160 (291)
.|-...-|.||||+|.++++|..+||-.-.|.+.
T Consensus 98 ~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 98 IIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred EEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 8888999999999999999999999998888763
No 120
>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=89.41 E-value=0.45 Score=44.03 Aligned_cols=38 Identities=21% Similarity=0.317 Sum_probs=35.8
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR 72 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~ 72 (291)
-.+.+.||.++.+..|||+|.|++-..+-||.+|.|..
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 47899999999999999999999999999999999965
No 121
>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=89.08 E-value=0.51 Score=34.19 Aligned_cols=36 Identities=17% Similarity=0.341 Sum_probs=30.8
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEc
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLS 71 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~ 71 (291)
.+++.|....-|.|||++|.+|++|+++..-...+.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 378888889999999999999999999887666663
No 122
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=89.07 E-value=0.48 Score=45.45 Aligned_cols=126 Identities=14% Similarity=0.072 Sum_probs=82.1
Q ss_pred eeeccCChhHHHHHHHhCCcEE--EcCCCCCCCCCCceE-EEEecCHHHHHHHHHHHHHHHhhhhccccccCCCCCceEE
Q 022837 48 AVIGKGGSTINDFQSQSGARIQ--LSRSHEFFPGTTDRI-IMISGTIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKL 124 (291)
Q Consensus 48 ~IIGk~G~~Ik~I~~~tga~I~--v~~~~~~~p~~~er~-v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~ 124 (291)
.+=||+--.+.+|++...|.+. +...+ ..++ -.+.|..-.-.++...+. .+++ ...
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~------gs~~~~~~~g~~~~F~k~~~~~~----~EFp-----------ae~ 451 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSST------GSIVETNGIGEKMSFSKKLSIPP----TEFP-----------AEI 451 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecC------CcEEEEeccCcchhhHHHhcCCc----ccCc-----------hhe
Confidence 5667777779999999999844 44322 2233 334566555565554443 2222 256
Q ss_pred EEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHH---HHHHHHHHHHHHHhc
Q 022837 125 RLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLD---EQMRALELILLKLSE 194 (291)
Q Consensus 125 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~---~v~~A~~~I~~~l~e 194 (291)
.+.||...+..|||-||..|++++...++.|++...-....+.--.-|.|.-+.. ++.-++.-+.+++.+
T Consensus 452 ~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 452 AFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred EEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 7889999999999999999999999999999997632221111122377776643 344456666666664
No 123
>PRK13764 ATPase; Provisional
Probab=89.00 E-value=0.34 Score=48.18 Aligned_cols=41 Identities=27% Similarity=0.357 Sum_probs=36.5
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCC
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHE 75 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~ 75 (291)
-...+.||...++.+|||+|.+|++|+++.|.+|.|....+
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 34668899999999999999999999999999999977543
No 124
>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=87.52 E-value=0.75 Score=33.32 Aligned_cols=36 Identities=17% Similarity=0.369 Sum_probs=29.5
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEE
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKI 157 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 157 (291)
...++.|....-|.|||++|+.|++|++.-.-...+
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 458888999999999999999999998876544433
No 125
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=86.46 E-value=0.82 Score=42.69 Aligned_cols=40 Identities=20% Similarity=0.244 Sum_probs=36.6
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
.-.+.+.||.++.++.|||+|.|++-..+-||.+|.|...
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 3568899999999999999999999999999999999753
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=86.18 E-value=1.1 Score=37.01 Aligned_cols=37 Identities=19% Similarity=0.283 Sum_probs=32.4
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEec
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISR 159 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 159 (291)
..+-++|-... |.-|||+|.+++++++..|-+|.+-.
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 35667777777 99999999999999999999999876
No 127
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=86.09 E-value=0.66 Score=44.84 Aligned_cols=39 Identities=18% Similarity=0.268 Sum_probs=36.2
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
-.+.+.||..+.+..|||+|.|++...+-||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 378899999999999999999999999999999999753
No 128
>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=85.19 E-value=0.88 Score=34.85 Aligned_cols=31 Identities=19% Similarity=0.402 Sum_probs=26.2
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCc
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR 67 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~ 67 (291)
+++.|-...-|.|||++|++|++|++.....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 6777788889999999999999999876543
No 129
>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=84.69 E-value=2.5 Score=37.57 Aligned_cols=30 Identities=30% Similarity=0.279 Sum_probs=23.6
Q ss_pred ceEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837 121 KTKLRLIVPNS-SCGSIIGKAGATIKSFMDD 150 (291)
Q Consensus 121 ~~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~ 150 (291)
.+...+.|..+ +-+.|||++|+.||+|...
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 36677788855 5599999999999988654
No 130
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=84.19 E-value=0.99 Score=42.95 Aligned_cols=38 Identities=21% Similarity=0.267 Sum_probs=35.4
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR 72 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~ 72 (291)
-.+.+.||.++.++.|||+|.|++-..+-||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 45789999999999999999999999999999999964
No 131
>PRK15494 era GTPase Era; Provisional
Probab=84.18 E-value=2.6 Score=38.97 Aligned_cols=29 Identities=24% Similarity=0.328 Sum_probs=22.7
Q ss_pred eEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837 122 TKLRLIVPNS-SCGSIIGKAGATIKSFMDD 150 (291)
Q Consensus 122 ~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~ 150 (291)
+...|.|..+ +-+.|||++|+.||+|...
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 5577778855 5599999999999987543
No 132
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.14 E-value=1.2 Score=32.34 Aligned_cols=29 Identities=24% Similarity=0.460 Sum_probs=23.7
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhC
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
+++.|....-|.+||++|.+|++|++.-.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence 55666668889999999999999888753
No 133
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=82.12 E-value=1.9 Score=34.68 Aligned_cols=36 Identities=31% Similarity=0.580 Sum_probs=31.4
Q ss_pred EEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 38 RFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 38 rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
++.|-.+.-|.+|||+|.++++|..+||-+-.+.+.
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 466677888999999999999999999988888653
No 134
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=81.65 E-value=1.8 Score=31.55 Aligned_cols=29 Identities=17% Similarity=0.367 Sum_probs=24.3
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
..++.|....-|.+||++|++|++|++.-
T Consensus 39 ~i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 39 GTQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred cEEEEEEECCCCceECCCchhHHHHHHHH
Confidence 36777777889999999999999987764
No 135
>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=81.59 E-value=1.4 Score=33.67 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=25.9
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhcc
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQ 152 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG 152 (291)
.+++.|....-|.|||++|++|++|++...
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 477888888899999999999999987644
No 136
>COG1159 Era GTPase [General function prediction only]
Probab=80.88 E-value=4.5 Score=36.54 Aligned_cols=30 Identities=37% Similarity=0.444 Sum_probs=22.8
Q ss_pred ceEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837 121 KTKLRLIVPNS-SCGSIIGKAGATIKSFMDD 150 (291)
Q Consensus 121 ~~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~ 150 (291)
.+...|.|+.+ +-+-||||+|++||+|-..
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 45666778854 5599999999999887543
No 137
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=80.39 E-value=3.4 Score=37.68 Aligned_cols=34 Identities=21% Similarity=0.318 Sum_probs=26.8
Q ss_pred CCceEEEEEecCCc-cceeeccCChhHHHHHHhcc
Q 022837 119 GTKTKLRLIVPNSS-CGSIIGKAGATIKSFMDDSQ 152 (291)
Q Consensus 119 ~~~~~~~i~VP~~~-vg~IIGk~G~~Ik~I~~~tG 152 (291)
...+..++.+|... ...||||||..|++|-++-+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 34578899999665 46889999999999976643
No 138
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=79.99 E-value=1.7 Score=37.69 Aligned_cols=32 Identities=31% Similarity=0.482 Sum_probs=26.7
Q ss_pred cEEEEEEecccccceeeccCChhHHHHHHHhC
Q 022837 34 PTYIRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 34 ~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
+..+++.|....-|.||||+|++|++|++...
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 34578888999999999999999988877543
No 139
>PRK03818 putative transporter; Validated
Probab=79.31 E-value=21 Score=35.39 Aligned_cols=136 Identities=18% Similarity=0.294 Sum_probs=75.8
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCCcEEEcC---CCCC-CC--C---CCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR---SHEF-FP--G---TTDRIIMISGTIDEILRAVDLVIDKLL 106 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~---~~~~-~p--~---~~er~v~I~G~~~~v~~A~~~I~~~i~ 106 (291)
..++.|+++. ++ |.+++++.......+.+.+ +... .| + ....++.|.|+.+++.++.+.+-..+.
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~ 279 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVD 279 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccC
Confidence 3566666433 33 6789999998877666532 1111 11 1 123568999999988777665532211
Q ss_pred hhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHH--HHhccceEE-EecCCCCC-CCC-----CceEEEEEcC
Q 022837 107 TELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSF--MDDSQAVIK-ISRLDHSY-YGL-----NDRLVTLTGT 177 (291)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I--~~~tGa~I~-i~~~~~~~-~~~-----~er~V~I~G~ 177 (291)
. . ...+........+++|+ ..++|| +++++ +++.|+.|. +.+.+... +.. .-..+.+.|+
T Consensus 280 ~----~-~~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~ 348 (552)
T PRK03818 280 T----S-LSTRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGR 348 (552)
T ss_pred c----c-ccccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEEC
Confidence 0 0 01111222344444454 367766 77877 566777643 33322211 111 1246899999
Q ss_pred HHHHHHHHHHH
Q 022837 178 LDEQMRALELI 188 (291)
Q Consensus 178 ~~~v~~A~~~I 188 (291)
++++++..+.+
T Consensus 349 ~~~i~~l~~~L 359 (552)
T PRK03818 349 PEAIDAVANVL 359 (552)
T ss_pred HHHHHHHHHHh
Confidence 99999977753
No 140
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=75.99 E-value=4.6 Score=34.48 Aligned_cols=69 Identities=14% Similarity=0.220 Sum_probs=43.3
Q ss_pred CceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCce-EEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 120 TKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDR-LVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 120 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er-~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
....+.+.+-.+..++|||+.|+++..||--+.+-++-.. +..-+ +|-+-+-.+.-+..+..+.+++.+
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~------g~~~~v~ldv~~yRerR~e~L~~LA~~~A~ 158 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIG------GKFKRVTLDVGDYRERRKETLIKLAERAAE 158 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhc------CcceEEEEEhhhHHHHHHHHHHHHHHHHHH
Confidence 4457777888888999999999999999988765444311 11122 234444444444445555555444
No 141
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=75.73 E-value=2.7 Score=36.52 Aligned_cols=30 Identities=23% Similarity=0.451 Sum_probs=26.0
Q ss_pred ceEEEEEecCCccceeeccCChhHHHHHHh
Q 022837 121 KTKLRLIVPNSSCGSIIGKAGATIKSFMDD 150 (291)
Q Consensus 121 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~ 150 (291)
...+++.|....=|.|||++|++|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 457889999999999999999999888653
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=74.79 E-value=7.8 Score=34.69 Aligned_cols=29 Identities=31% Similarity=0.463 Sum_probs=22.1
Q ss_pred eEEEEEecCC-ccceeeccCChhHHHHHHh
Q 022837 122 TKLRLIVPNS-SCGSIIGKAGATIKSFMDD 150 (291)
Q Consensus 122 ~~~~i~VP~~-~vg~IIGk~G~~Ik~I~~~ 150 (291)
+...|.|..+ +-+.|||++|++||+|...
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 5666777744 5599999999999887543
No 143
>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=73.32 E-value=4.6 Score=35.88 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=24.2
Q ss_pred EEEEEEeccc-ccceeeccCChhHHHHHHHh
Q 022837 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQSQS 64 (291)
Q Consensus 35 ~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~t 64 (291)
+...++|..+ +-+.||||+|+.||+|..+.
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 78999999999999886653
No 144
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=71.75 E-value=15 Score=35.70 Aligned_cols=103 Identities=17% Similarity=0.255 Sum_probs=72.9
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHhhhhccccc
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLLTELHAEDQ 114 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~ 114 (291)
-.+.|.||...+-.|||.||..|++.+.+.++.|++...-+ ++. + .+.
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~-~~q-------------s-----------~~~------- 496 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK-FGQ-------------S-----------QWH------- 496 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh-cch-------------h-----------hhh-------
Confidence 45778999999999999999999999999999999864211 000 0 111
Q ss_pred cCCCCCceEEEEEecCCccceeeccCChhHHHHHHhc----cceEEEecCCCCCCCCCceEEEEEcCHHHHHH
Q 022837 115 ADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDS----QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMR 183 (291)
Q Consensus 115 ~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t----Ga~I~i~~~~~~~~~~~er~V~I~G~~~~v~~ 183 (291)
.-+-+..|..-.+.|+|++......+++.. ...|++.+ . .-++.++-|-.+-+.+
T Consensus 497 -------dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~------~-~~sI~~v~~~~~~I~r 555 (657)
T COG5166 497 -------DNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP------Q-STSIFTVDIYSDEIER 555 (657)
T ss_pred -------cceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC------C-ceEEEEEcccccHHHH
Confidence 135566888999999999998888887553 34566654 2 3458888777665543
No 145
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=69.92 E-value=8 Score=38.95 Aligned_cols=37 Identities=30% Similarity=0.540 Sum_probs=32.2
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcEEEcCC
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRS 73 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~ 73 (291)
=+++|-.+.-|.||||+|.++++|.++||-+-.|.+.
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 3567777888999999999999999999998888764
No 146
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=66.91 E-value=11 Score=36.74 Aligned_cols=36 Identities=31% Similarity=0.545 Sum_probs=31.3
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcEEEcC
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSR 72 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~ 72 (291)
=.++|-.+.-|.+|||+|++.+.|.++||-.-.|-+
T Consensus 101 GEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 101 GEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred ceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 356777888899999999999999999998777765
No 147
>PRK15494 era GTPase Era; Provisional
Probab=66.20 E-value=7.8 Score=35.82 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=23.5
Q ss_pred EEEEEEeccc-ccceeeccCChhHHHHHHH
Q 022837 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQSQ 63 (291)
Q Consensus 35 ~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~ 63 (291)
+...|+|..+ +-+.||||+|..||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 5566778766 8899999999999987654
No 148
>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=66.10 E-value=19 Score=26.15 Aligned_cols=54 Identities=11% Similarity=0.043 Sum_probs=41.9
Q ss_pred CChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837 140 AGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (291)
Q Consensus 140 ~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~ 193 (291)
|=..+.++-+..|++++....|...-...+.+++++|+..++..|.+.++.+|.
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 445678888888999988765544334568999999999999999999988775
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=65.67 E-value=8.1 Score=34.57 Aligned_cols=29 Identities=24% Similarity=0.479 Sum_probs=22.2
Q ss_pred EEEEEEeccc-ccceeeccCChhHHHHHHH
Q 022837 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQSQ 63 (291)
Q Consensus 35 ~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~ 63 (291)
+...+.|..+ +-+.||||+|++||+|...
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 4555666654 7799999999999987654
No 150
>COG1159 Era GTPase [General function prediction only]
Probab=65.03 E-value=9 Score=34.66 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=22.8
Q ss_pred EEEEEEeccc-ccceeeccCChhHHHHHHH
Q 022837 35 TYIRFLVSNP-LAGAVIGKGGSTINDFQSQ 63 (291)
Q Consensus 35 ~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~ 63 (291)
+...++|..+ +-|.||||+|++||+|-..
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 4555777765 8899999999999877554
No 151
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=64.75 E-value=4 Score=34.86 Aligned_cols=36 Identities=22% Similarity=0.315 Sum_probs=29.6
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEE
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQL 70 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v 70 (291)
-.+.+-+..+..|.+||+.|.++..||--+..-++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 345666777779999999999999999998866655
No 152
>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=63.28 E-value=83 Score=31.31 Aligned_cols=140 Identities=17% Similarity=0.236 Sum_probs=74.9
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEc---CCCCC-CCCC-----CceEEEEecCHHHHHHHHHHHHHHH
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLS---RSHEF-FPGT-----TDRIIMISGTIDEILRAVDLVIDKL 105 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~---~~~~~-~p~~-----~er~v~I~G~~~~v~~A~~~I~~~i 105 (291)
....+.|+.. ..++ |.+++++.......+.+. ++++. .|.. ....+.+.|+.+++.++.+.+-..+
T Consensus 218 ~~r~~~V~~~--s~li---GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~ 292 (562)
T TIGR03802 218 VGRAYRVNRA--SSLI---GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEV 292 (562)
T ss_pred eeEEEEECCC--cccC---CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCcc
Confidence 3445566654 2233 557888887775544442 11111 1111 2346899999999887766653222
Q ss_pred hhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHH------HhccceEEE-ecCCCCCCC------CCceEE
Q 022837 106 LTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFM------DDSQAVIKI-SRLDHSYYG------LNDRLV 172 (291)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~------~~tGa~I~i-~~~~~~~~~------~~er~V 172 (291)
... . ..+ ......++++|+ ..++|| +++++. ++.|+.|.- .+.+...+. ..-..+
T Consensus 293 ~~~---~--~~~-~~~~~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~L 360 (562)
T TIGR03802 293 QEV---E--GLD-VPMETKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVV 360 (562)
T ss_pred CCc---c--ccC-CceEEEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEE
Confidence 111 0 011 112244444553 466665 788886 267777443 332221111 112468
Q ss_pred EEEcCHHHHHHHHHHHHHH
Q 022837 173 TLTGTLDEQMRALELILLK 191 (291)
Q Consensus 173 ~I~G~~~~v~~A~~~I~~~ 191 (291)
.+.|++++++++.+.+-..
T Consensus 361 lV~G~~~~l~~~~~~lG~~ 379 (562)
T TIGR03802 361 TLVGTPQDVDRAAKQLGYA 379 (562)
T ss_pred EEEeCHHHHHHHHHHcCCc
Confidence 9999999999977765433
No 153
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=61.21 E-value=19 Score=33.26 Aligned_cols=53 Identities=11% Similarity=0.097 Sum_probs=45.0
Q ss_pred EecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 022837 127 IVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELIL 189 (291)
Q Consensus 127 ~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~ 189 (291)
+-+.+..-.|.|..+.+++.|.+..|++|.... +.++|+|+...|..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEechHHHHHHHHHHh
Confidence 344677789999999999999999999888754 57999999878888888877
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=60.83 E-value=9.5 Score=32.74 Aligned_cols=31 Identities=26% Similarity=0.489 Sum_probs=25.0
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCc
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGAR 67 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~ 67 (291)
+++.|....-|.+||++|.+|+++++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 5555666888999999999999998876543
No 155
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=60.41 E-value=10 Score=32.27 Aligned_cols=31 Identities=23% Similarity=0.439 Sum_probs=26.2
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCC
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGA 66 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga 66 (291)
.+++.|....-|.|||++|.+|++|++.-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 3778888888999999999999998887643
No 156
>CHL00048 rps3 ribosomal protein S3
Probab=59.72 E-value=10 Score=32.74 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=25.9
Q ss_pred EEEEEecccccceeeccCChhHHHHHHHhCC
Q 022837 36 YIRFLVSNPLAGAVIGKGGSTINDFQSQSGA 66 (291)
Q Consensus 36 ~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga 66 (291)
.+++.|-...-|.|||++|.+|++|++...-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k 97 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQK 97 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHHH
Confidence 4677777788899999999999999987643
No 157
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=57.56 E-value=11 Score=32.59 Aligned_cols=32 Identities=19% Similarity=0.354 Sum_probs=26.6
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhCCcE
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSGARI 68 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I 68 (291)
+++.|....-|.|||++|..|++|++...-.+
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 67777778889999999999999998765443
No 158
>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=57.33 E-value=12 Score=31.75 Aligned_cols=30 Identities=20% Similarity=0.416 Sum_probs=25.8
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
...++.|....-|.|||++|..|++|++.-
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 457888888999999999999999987654
No 159
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=56.46 E-value=13 Score=32.00 Aligned_cols=30 Identities=20% Similarity=0.409 Sum_probs=24.8
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhcc
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQ 152 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG 152 (291)
...+.|....-|.+||++|++|+++++.-.
T Consensus 41 ~i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 41 GTRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred cEEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 366777778899999999999999887653
No 160
>CHL00048 rps3 ribosomal protein S3
Probab=55.20 E-value=14 Score=31.98 Aligned_cols=30 Identities=13% Similarity=0.176 Sum_probs=25.7
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
...++.|....-|.|||++|++|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 457788888888999999999999998765
No 161
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=53.54 E-value=14 Score=31.95 Aligned_cols=30 Identities=13% Similarity=0.346 Sum_probs=25.3
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
...++.|....-|.|||++|..|++|++.-
T Consensus 44 ~~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 44 IRTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred CcEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 357888888889999999999999887654
No 162
>cd01568 QPRTase_NadC Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other.
Probab=51.03 E-value=1.8e+02 Score=25.88 Aligned_cols=61 Identities=13% Similarity=0.084 Sum_probs=43.1
Q ss_pred ccceeeccCChhHHHHHHhc-cceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 132 SCGSIIGKAGATIKSFMDDS-QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 132 ~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
.-+.+-| =....+|-+.. ++.+...-.+...-...+.+++|+|+...+..++..++.+|+-
T Consensus 37 ~~~v~~G--~~~~~~i~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~l~~~Er~~ln~L~~ 98 (269)
T cd01568 37 EEGVLAG--LEVAEEVFELLDGIEVEWLVKDGDRVEAGQVLLEVEGPARSLLTAERVALNLLQR 98 (269)
T ss_pred CCEEEEC--HHHHHHHHHHhCCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 3344443 34567777777 8887665544433345789999999999999999988877754
No 163
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=50.46 E-value=50 Score=30.60 Aligned_cols=53 Identities=15% Similarity=0.171 Sum_probs=44.0
Q ss_pred EecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837 40 LVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (291)
Q Consensus 40 lvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~ 102 (291)
+-+...+-.+.|..+.+++.|++.+|+.|... .+.+.|.|....+..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r----------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVAR----------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeC----------CceEEEEechHHHHHHHHHHh
Confidence 33466788999999999999999999988884 256999999778888877776
No 164
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=48.22 E-value=20 Score=32.86 Aligned_cols=32 Identities=19% Similarity=0.362 Sum_probs=26.2
Q ss_pred cEEEEEEeccc-ccceeeccCChhHHHHHHHhC
Q 022837 34 PTYIRFLVSNP-LAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 34 ~~~~rilvp~~-~vG~IIGk~G~~Ik~I~~~tg 65 (291)
.+..++.||.. +.-.||||+|..|++|-++-+
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 46778899987 677899999999999987644
No 165
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=46.55 E-value=59 Score=22.14 Aligned_cols=36 Identities=14% Similarity=-0.011 Sum_probs=24.1
Q ss_pred EEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 022837 155 IKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK 191 (291)
Q Consensus 155 I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~ 191 (291)
+.+......||. .--.+.|+|+..+|+.|+..|.+.
T Consensus 25 V~i~d~f~gCPq-~~~~l~i~Gdvs~Ve~Al~~i~~~ 60 (61)
T cd07055 25 VFVSDIFGSCPQ-HMITLAIFGETSAVELAMREIEED 60 (61)
T ss_pred eEEEEecCCCCC-ceEEEEEEecHHHHHHHHHHHhhc
Confidence 444433334444 334677999999999999988653
No 166
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=43.86 E-value=25 Score=30.32 Aligned_cols=29 Identities=34% Similarity=0.538 Sum_probs=24.3
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhC
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
+++.|....-|.|||++|.+|++|++...
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 66777777789999999999999987654
No 167
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=43.49 E-value=74 Score=22.37 Aligned_cols=42 Identities=19% Similarity=0.155 Sum_probs=29.3
Q ss_pred hhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 022837 142 ATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILL 190 (291)
Q Consensus 142 ~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~ 190 (291)
..|.+|-+.++|+|.=... +.-+++++|+++.+...+.++..
T Consensus 17 ~ei~~l~~~f~a~ivd~~~-------~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 17 SEILQLAEIFRARIVDVSP-------DSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHTT-EEEEEET-------TEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHhCCEEEEECC-------CEEEEEEcCCHHHHHHHHHHhhh
Confidence 4578888999998544331 45789999999999877766543
No 168
>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=43.25 E-value=2.4e+02 Score=25.11 Aligned_cols=55 Identities=13% Similarity=0.002 Sum_probs=41.6
Q ss_pred CChhHHHHHHhc--cceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 140 AGATIKSFMDDS--QAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 140 ~G~~Ik~I~~~t--Ga~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
|-....+|-+.. ++++...-.+...-...+.+++|+|+...+..++..++.+|+-
T Consensus 43 G~~~~~~i~~~~~~~l~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~L~~ 99 (268)
T cd01572 43 GLPVAEEVFELLDPGIEVEWLVKDGDRVEPGQVLATVEGPARSLLTAERTALNFLQR 99 (268)
T ss_pred CHHHHHHHHHHcCCCeEEEEEeCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 345567888877 8888666544433345789999999999999999988877753
No 169
>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=43.23 E-value=87 Score=25.87 Aligned_cols=55 Identities=11% Similarity=0.155 Sum_probs=40.6
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l 192 (291)
.+.++.++....- +.+.+|.+-.|+-+.+. ++..|.|-|..+.|.+|+.-+..+-
T Consensus 113 ~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe---------e~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 113 ETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE---------EDDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred eeEEEecCccchH-------HHHHHHHHHhceeEEec---------CCcEEEEeccHHHHHHHHHHHHHHh
Confidence 4555555544432 45788999999988882 3457999999999999999887654
No 170
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=41.62 E-value=28 Score=30.00 Aligned_cols=29 Identities=31% Similarity=0.573 Sum_probs=24.6
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
.+++.|....-|.|||++|..|++|++.-
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 46788888888999999999999997554
No 171
>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=39.74 E-value=78 Score=22.87 Aligned_cols=70 Identities=16% Similarity=0.170 Sum_probs=45.7
Q ss_pred CcEEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHHHHHh
Q 022837 33 KPTYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVIDKLL 106 (291)
Q Consensus 33 ~~~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~~~i~ 106 (291)
......+..-++ |-+= |=.-+.++=+..++++.+...+...-...+.++.+.|...++..|.+.++..|.
T Consensus 16 ~~~~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 16 KTGTATIIARED--GVLA--GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SEEEEEEEESSS--EEE---SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CEEEEEEEeCCC--EEEE--CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 334444444433 3332 335668888888988888743322222357899999999999999999887664
No 172
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=39.22 E-value=52 Score=25.06 Aligned_cols=47 Identities=13% Similarity=0.082 Sum_probs=34.5
Q ss_pred HHHHh-ccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837 146 SFMDD-SQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSEDTLYS 199 (291)
Q Consensus 146 ~I~~~-tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e~~~~~ 199 (291)
.|-.+ .++.|-|.+. -...+.|+|+..+|+.|+..+.+.+++.-.+.
T Consensus 57 DIA~Kaa~V~igF~DR-------FsGslvitGdvs~Ve~Al~~V~~~l~~~L~F~ 104 (111)
T PRK15468 57 DLALKAADVHIGFLDR-------FSGALVIYGSVGAVEEALSQTVSGLGRLLNYT 104 (111)
T ss_pred HhhhhccCcEEeeeec-------cceeEEEEccHHHHHHHHHHHHHHHHhhcCcc
Confidence 34333 3466666652 23569999999999999999999999865554
No 173
>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=38.17 E-value=3e+02 Score=24.74 Aligned_cols=54 Identities=11% Similarity=0.008 Sum_probs=43.1
Q ss_pred CChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837 140 AGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (291)
Q Consensus 140 ~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~ 193 (291)
|-....++-+..|+++.+...+...-...+.+++++|+...+..|++.++.+|+
T Consensus 47 G~~~~~~i~~~l~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~alN~l~ 100 (277)
T TIGR01334 47 GVSEAAKLLKQLGASIDYAVPSGSRALAGTLLLEAKGSAGQLHQGWKSAQSVLE 100 (277)
T ss_pred CHHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEecHHHHHHHHHHHHHHHH
Confidence 345678888888999988876654445678999999999999999998877665
No 174
>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=36.39 E-value=2.5e+02 Score=23.26 Aligned_cols=101 Identities=16% Similarity=0.081 Sum_probs=58.2
Q ss_pred EEEec--CHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEEEecCCccceeeccCChhHHHHHHhccceEEEecCCC
Q 022837 85 IMISG--TIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVIKISRLDH 162 (291)
Q Consensus 85 v~I~G--~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~ 162 (291)
+.++| +.+++..|.+.+.+.|.+... . .......+++-.+-.-..+.=| .++.|....+-++...++..
T Consensus 58 ivitGaks~~~~~~a~~~~~~~L~~~g~-~---~~~~~~~~v~NIvas~~l~~~i-----~L~~la~~~~~~~~YePe~f 128 (174)
T cd00652 58 MVITGAKSEEDAKLAARKYARILQKLGF-P---VEKFPEFKVQNIVASCDLGFPI-----RLEELALKHPENASYEPELF 128 (174)
T ss_pred EEEEecCCHHHHHHHHHHHHHHHHHcCC-C---ccccCceEEEEEEEEEECCCcc-----cHHHHHhhhhcccEECCccC
Confidence 77888 688999999999877754411 1 0012233444444333333322 46777666554444444211
Q ss_pred CC-------CC-----CCceEEEEEcC--HHHHHHHHHHHHHHHhc
Q 022837 163 SY-------YG-----LNDRLVTLTGT--LDEQMRALELILLKLSE 194 (291)
Q Consensus 163 ~~-------~~-----~~er~V~I~G~--~~~v~~A~~~I~~~l~e 194 (291)
+. +. -....|+|+|. .+.+.+|...|..+|.+
T Consensus 129 pgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L~~ 174 (174)
T cd00652 129 PGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPILKE 174 (174)
T ss_pred ceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHhC
Confidence 00 00 12346888887 68899999999988753
No 175
>PRK06106 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=35.16 E-value=3.1e+02 Score=24.72 Aligned_cols=53 Identities=13% Similarity=0.048 Sum_probs=38.9
Q ss_pred hhHHHHHHhccce--EEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 142 ATIKSFMDDSQAV--IKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 142 ~~Ik~I~~~tGa~--I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
...+++-+..|.. +.+...+...-...+.+++++|+...+..|++.++.+|+-
T Consensus 57 ~~a~~vf~~~~~~~~~~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~L~~ 111 (281)
T PRK06106 57 DLARLAFRLVDPEIEMRRHLPDGAAVAPGDVIATISGPARGLLTAERTALNFLCH 111 (281)
T ss_pred HHHHHHHHHhCCceEEEEEeCCCCEEcCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 4567888888855 5555444433345789999999999999999988877753
No 176
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=32.74 E-value=2.2e+02 Score=25.61 Aligned_cols=73 Identities=15% Similarity=0.226 Sum_probs=46.3
Q ss_pred eEEEEEecCCc--cceeeccCCh------hHHHHHHhccce--EEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHH
Q 022837 122 TKLRLIVPNSS--CGSIIGKAGA------TIKSFMDDSQAV--IKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLK 191 (291)
Q Consensus 122 ~~~~i~VP~~~--vg~IIGk~G~------~Ik~I~~~tGa~--I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~ 191 (291)
.|...++|.+. -..++-|... ...++-+..+.. +.....+...-...+.+++++|+..++..|++.++.+
T Consensus 23 lTt~~~i~~~~~~~~~~~ar~~gv~~G~~~a~~i~~~~~~~~~v~~~~~dG~~v~~g~~i~~~~G~~~~ll~~er~~ln~ 102 (277)
T PRK08072 23 VTSQLIFPDNLLGEGVFLAKDTGVFAGRLVIEEGYKLLDERIEVELHKKDGDLVKKGEIIATVQGPVASLLTGERVILNL 102 (277)
T ss_pred CCcccccCCCCeEEEEEEecCCEEEECHHHHHHHHHHcCCceEEEEEeCCCCEEcCCCEEEEEEECHHHHHHHHHHHHHH
Confidence 34444566552 2445544433 346777766644 5555444333345688999999999999999988877
Q ss_pred Hhc
Q 022837 192 LSE 194 (291)
Q Consensus 192 l~e 194 (291)
|+-
T Consensus 103 l~~ 105 (277)
T PRK08072 103 IQR 105 (277)
T ss_pred HHH
Confidence 653
No 177
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=32.47 E-value=1.8e+02 Score=26.09 Aligned_cols=54 Identities=11% Similarity=0.125 Sum_probs=42.0
Q ss_pred ChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 141 GATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 141 G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
-....+|-+..|+++.+.-.+...-...+.+++++|+...+..++..++.+|+-
T Consensus 46 ~~~a~~i~~~l~~~~~~~~~dG~~v~~g~~i~~i~G~a~~ll~~Er~~ln~l~~ 99 (273)
T PRK05848 46 EKYALELLEMTGIECVFTIKDGERFKKGDILMEIEGDFSMLLKVERTLLNLLQH 99 (273)
T ss_pred HHHHHHHHHHcCCEEEEEcCCCCEecCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 345678888889888876655444445789999999999999999988877753
No 178
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=32.47 E-value=44 Score=29.19 Aligned_cols=29 Identities=28% Similarity=0.526 Sum_probs=23.5
Q ss_pred EEEEecccccceeeccCChhHHHHHHHhC
Q 022837 37 IRFLVSNPLAGAVIGKGGSTINDFQSQSG 65 (291)
Q Consensus 37 ~rilvp~~~vG~IIGk~G~~Ik~I~~~tg 65 (291)
+++.|-...-|.|||++|..|++|++...
T Consensus 64 i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 64 VRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 55666667779999999999999888764
No 179
>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=31.78 E-value=3.7e+02 Score=23.95 Aligned_cols=52 Identities=8% Similarity=0.015 Sum_probs=40.1
Q ss_pred hhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837 142 ATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (291)
Q Consensus 142 ~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~ 193 (291)
....++-+..++++.+.-.+...-...+.+++|+|+...+..++..++.+|+
T Consensus 45 ~~~~~~~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~ll~~Er~~ln~l~ 96 (272)
T cd01573 45 EEAARILELLGLEVDLAAASGSRVAAGAVLLEAEGPAAALHLGWKVAQTLLE 96 (272)
T ss_pred HHHHHHHHHcCcEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHH
Confidence 4567888888888876654444334578999999999999999998887665
No 180
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.70 E-value=1.9e+02 Score=23.32 Aligned_cols=44 Identities=20% Similarity=0.256 Sum_probs=34.7
Q ss_pred hhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 142 ATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 142 ~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
+.++.|.+-.|+-|.+.. ...|.|-|..+.|.+|+..|..+-.+
T Consensus 126 eRlqDi~E~hgvIiE~~E---------~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE---------YDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEeee---------ccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 356777788888888763 34799999999999999999877543
No 181
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=29.18 E-value=1.1e+02 Score=23.36 Aligned_cols=48 Identities=21% Similarity=0.268 Sum_probs=33.1
Q ss_pred ccCChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcC---HHHHHHHHHHHHHHHhcC
Q 022837 138 GKAGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGT---LDEQMRALELILLKLSED 195 (291)
Q Consensus 138 Gk~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~---~~~v~~A~~~I~~~l~e~ 195 (291)
|+||.+++.. .|.|.|...+ +.-+|+...+ ..+.+.|+..+.++|.+.
T Consensus 23 GpGGQ~VNk~--~s~V~l~h~p--------tgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~ 73 (113)
T PF00472_consen 23 GPGGQNVNKT--NSKVRLRHIP--------TGIVVKCQESRSQHQNREDALEKLREKLDEA 73 (113)
T ss_dssp SSSSCHHHSS--SEEEEEEETT--------TTEEEEEESSSSHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCccccc--CCEEEEEEec--------ccEEEEEcccCCHHHHHHHHHHHHHHHHHHH
Confidence 8999998853 3557776654 2234444444 677788999998888764
No 182
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=28.80 E-value=54 Score=28.68 Aligned_cols=30 Identities=27% Similarity=0.531 Sum_probs=24.5
Q ss_pred eEEEEEecCCccceeeccCChhHHHHHHhc
Q 022837 122 TKLRLIVPNSSCGSIIGKAGATIKSFMDDS 151 (291)
Q Consensus 122 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t 151 (291)
..+++.|....-+.|||++|..|++|++..
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 356777777888999999999999987664
No 183
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating)
Probab=27.55 E-value=2.4e+02 Score=25.08 Aligned_cols=53 Identities=9% Similarity=0.055 Sum_probs=40.0
Q ss_pred hhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 142 ATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 142 ~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
....+|-+..++.+...-.+...-...+.+++|+|+...+..++..++.+|+-
T Consensus 43 ~~~~~i~~~~~~~v~~~~~dG~~v~~g~~i~~i~G~~~~il~~Er~~ln~l~~ 95 (265)
T TIGR00078 43 PVARRVFEQLGVQVEWLVKDGDRVEPGEVVAEVEGPARSLLTAERTALNFLGR 95 (265)
T ss_pred HHHHHHHHHcCeEEEEEeCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHHH
Confidence 45677778888887665544433345789999999999999999988877753
No 184
>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=26.75 E-value=4.7e+02 Score=23.50 Aligned_cols=53 Identities=9% Similarity=0.140 Sum_probs=40.4
Q ss_pred hhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 022837 142 ATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLSE 194 (291)
Q Consensus 142 ~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~e 194 (291)
....++-+..++++...-.+...-...+.++++.|+...+..|+..++.+|+-
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 34567777788888886544443445789999999999999999988876653
No 185
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=26.03 E-value=1.2e+02 Score=23.20 Aligned_cols=29 Identities=28% Similarity=0.353 Sum_probs=25.4
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhcCcccC
Q 022837 171 LVTLTGTLDEQMRALELILLKLSEDTLYS 199 (291)
Q Consensus 171 ~V~I~G~~~~v~~A~~~I~~~l~e~~~~~ 199 (291)
.+.|+|+..+|+.|++...+.+++...+.
T Consensus 75 ~vii~GdvsaV~aAl~a~~~~~~~~~~f~ 103 (110)
T cd07046 75 ALVITGDVSEVESALEAVVDYLRETLGFT 103 (110)
T ss_pred EEEEEECHHHHHHHHHHHHHHHhhccCce
Confidence 67899999999999999999999865543
No 186
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=23.96 E-value=1.3e+02 Score=21.01 Aligned_cols=28 Identities=14% Similarity=0.132 Sum_probs=24.7
Q ss_pred CceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 022837 168 NDRLVTLTGTLDEQMRALELILLKLSED 195 (291)
Q Consensus 168 ~er~V~I~G~~~~v~~A~~~I~~~l~e~ 195 (291)
..-.+.|+|+..+|+.|++...+.+.+.
T Consensus 38 g~~~~~i~G~vs~V~~Av~a~~~~~~~~ 65 (75)
T PF00936_consen 38 GKVTVIITGDVSAVKAAVDAAEEAAGKK 65 (75)
T ss_dssp TEEEEEEEESHHHHHHHHHHHHHHHHHT
T ss_pred CeEEEEEEECHHHHHHHHHHHHHHHhhc
Confidence 4568999999999999999999988774
No 187
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=23.70 E-value=1.4e+02 Score=20.59 Aligned_cols=51 Identities=12% Similarity=0.126 Sum_probs=34.3
Q ss_pred ChhHHHHHHhccceEEEecCCC-CCC--CCCceEEEEEcCHHHHHHHHHHHHHH
Q 022837 141 GATIKSFMDDSQAVIKISRLDH-SYY--GLNDRLVTLTGTLDEQMRALELILLK 191 (291)
Q Consensus 141 G~~Ik~I~~~tGa~I~i~~~~~-~~~--~~~er~V~I~G~~~~v~~A~~~I~~~ 191 (291)
...|.++.++++..+.|....- ... ....=.+.+.|+.+++++|+..+.+.
T Consensus 16 ~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~~ 69 (76)
T PF09383_consen 16 EPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLREQ 69 (76)
T ss_dssp SCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT
T ss_pred chHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHHC
Confidence 3458899999999998875211 000 11334689999999999999988764
No 188
>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=23.62 E-value=5.5e+02 Score=23.19 Aligned_cols=53 Identities=8% Similarity=-0.021 Sum_probs=39.6
Q ss_pred ChhHHHHHHhccceEE--EecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837 141 GATIKSFMDDSQAVIK--ISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (291)
Q Consensus 141 G~~Ik~I~~~tGa~I~--i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~ 193 (291)
-....+|-+..++++. +...+...-...+.++++.|+..++..|++.++.+|+
T Consensus 58 ~~~a~~i~~~~~~~~~~~~~~~dG~~v~~g~~i~~~~G~a~~ll~~eR~~lN~l~ 112 (288)
T PRK07428 58 LPIAARVFQLLDPQVSFTPLVAEGAACESGQVVAEIEGPLDALLMGERVALNLAM 112 (288)
T ss_pred HHHHHHHHHHcCCcEEEEEEcCCCCEecCCCEEEEEEEcHHHHHHHHHHHHHHHH
Confidence 4566888888887776 4334433334568899999999999999998887765
No 189
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.03 E-value=2.6e+02 Score=23.10 Aligned_cols=52 Identities=17% Similarity=0.349 Sum_probs=39.9
Q ss_pred EEEEEEecccccceeeccCChhHHHHHHHhCCcEEEcCCCCCCCCCCceEEEEecCHHHHHHHHHHHH
Q 022837 35 TYIRFLVSNPLAGAVIGKGGSTINDFQSQSGARIQLSRSHEFFPGTTDRIIMISGTIDEILRAVDLVI 102 (291)
Q Consensus 35 ~~~rilvp~~~vG~IIGk~G~~Ik~I~~~tga~I~v~~~~~~~p~~~er~v~I~G~~~~v~~A~~~I~ 102 (291)
-++|+.++.... =+.+..|.+-.|+-+.+. ++..|.|.|..+.|.+|++.+.
T Consensus 113 ~~iRv~l~~~i~-------~erl~ei~E~~gvI~Efe---------e~~~V~I~Gdke~Ik~aLKe~s 164 (169)
T PF09869_consen 113 ETIRVKLKKPIQ-------EERLQEISEWHGVIFEFE---------EDDKVVIEGDKERIKKALKEFS 164 (169)
T ss_pred eeEEEecCccch-------HHHHHHHHHHhceeEEec---------CCcEEEEeccHHHHHHHHHHHH
Confidence 346666665542 256789999999999992 2456999999999999999886
No 190
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=22.73 E-value=2.5e+02 Score=23.47 Aligned_cols=106 Identities=20% Similarity=0.213 Sum_probs=52.6
Q ss_pred EEEec--CHHHHHHHHHHHHHHHhhhhccccccCCCCCceEEEEEec-------CCccceeeccCChhHHHHHHhc-cce
Q 022837 85 IMISG--TIDEILRAVDLVIDKLLTELHAEDQADDVGTKTKLRLIVP-------NSSCGSIIGKAGATIKSFMDDS-QAV 154 (291)
Q Consensus 85 v~I~G--~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~i~VP-------~~~vg~IIGk~G~~Ik~I~~~t-Ga~ 154 (291)
+.++| +.+++..|.+.+.+.|..... .......++++=.|- -+.-..-||-+.+++..=-+++ |--
T Consensus 64 ~VcTGaKs~ed~~~av~~~~~~L~~~g~----~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLV 139 (185)
T COG2101 64 VVCTGAKSVEDVHRAVKKLAKKLKDGGI----DIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLV 139 (185)
T ss_pred EEEeccCcHHHHHHHHHHHHHHHHhcCc----CcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeE
Confidence 55566 568899999988877766311 111222333333333 2333333444443322211111 111
Q ss_pred EEEecCCCCCCCCCceEEEEEcC--HHHHHHHHHHHHHHHhc
Q 022837 155 IKISRLDHSYYGLNDRLVTLTGT--LDEQMRALELILLKLSE 194 (291)
Q Consensus 155 I~i~~~~~~~~~~~er~V~I~G~--~~~v~~A~~~I~~~l~e 194 (291)
-++....-..--.....+.|||. ++.+..|.+.|.+.|.+
T Consensus 140 YRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~~L~e 181 (185)
T COG2101 140 YRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSRLEE 181 (185)
T ss_pred EEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHHHHHHHH
Confidence 11111000000012234677775 88999999999999987
No 191
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=22.49 E-value=4.5e+02 Score=21.81 Aligned_cols=44 Identities=11% Similarity=0.032 Sum_probs=33.1
Q ss_pred CChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 022837 140 AGATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILL 190 (291)
Q Consensus 140 ~G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~ 190 (291)
....|.+|.+.++|+|-=... +.-+++++|+++.+.+-+.++..
T Consensus 97 ~r~ei~~~~~~f~a~ivdv~~-------~~~~ie~tG~~~ki~a~~~~l~~ 140 (174)
T CHL00100 97 TRPEILEIAQIFRAKVVDLSE-------ESLILEVTGDPGKIVAIEQLLEK 140 (174)
T ss_pred CHHHHHHHHHHhCCEEEEecC-------CEEEEEEcCCHHHHHHHHHHhhh
Confidence 445688899999998554331 34689999999999987777654
No 192
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=21.07 E-value=2.7e+02 Score=19.19 Aligned_cols=24 Identities=21% Similarity=0.199 Sum_probs=20.1
Q ss_pred CceEEEEEcCHHHHHHHHHHHHHH
Q 022837 168 NDRLVTLTGTLDEQMRALELILLK 191 (291)
Q Consensus 168 ~er~V~I~G~~~~v~~A~~~I~~~ 191 (291)
....+.|+|+++.++....+|.++
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 346799999999999999888764
No 193
>cd06169 BMC Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypo
Probab=21.06 E-value=2.2e+02 Score=19.03 Aligned_cols=25 Identities=12% Similarity=-0.012 Sum_probs=20.8
Q ss_pred CCceEEEEEcCHHHHHHHHHHHHHH
Q 022837 167 LNDRLVTLTGTLDEQMRALELILLK 191 (291)
Q Consensus 167 ~~er~V~I~G~~~~v~~A~~~I~~~ 191 (291)
...-.+.|+|+...|+.|.+...+.
T Consensus 37 ~g~~~~~i~G~~s~V~~A~~a~~~~ 61 (62)
T cd06169 37 GGLVTLIIRGDVSAVKAAVEAAEQA 61 (62)
T ss_pred CcEEEEEEEECHHHHHHHHHHHHhh
Confidence 3567899999999999999887653
No 194
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=20.96 E-value=94 Score=25.58 Aligned_cols=62 Identities=18% Similarity=0.240 Sum_probs=37.5
Q ss_pred EEEEEecCCccceeeccCChhHHHHHHhccceE-EEecCCCCC--CC-----CCceEEEEEcCHHHHHHHHHHHH
Q 022837 123 KLRLIVPNSSCGSIIGKAGATIKSFMDDSQAVI-KISRLDHSY--YG-----LNDRLVTLTGTLDEQMRALELIL 189 (291)
Q Consensus 123 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I-~i~~~~~~~--~~-----~~er~V~I~G~~~~v~~A~~~I~ 189 (291)
..++..-..++|+=||- -+++.+|||.| -|.++.+.. |+ ..-.++.+.|+..++.++.....
T Consensus 89 ~~~i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 89 WFKIEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eeeeecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 33444444555555554 35789999984 444433221 22 12357899999999988876653
No 195
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=20.76 E-value=2.4e+02 Score=21.38 Aligned_cols=48 Identities=13% Similarity=0.042 Sum_probs=32.2
Q ss_pred HHhccceEEEecCCC------CCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 022837 148 MDDSQAVIKISRLDH------SYYGLNDRLVTLTG-TLDEQMRALELILLKLSED 195 (291)
Q Consensus 148 ~~~tGa~I~i~~~~~------~~~~~~er~V~I~G-~~~~v~~A~~~I~~~l~e~ 195 (291)
-..+.+.|-+.++-. ..+-+.+-++.|.| ++..|+.|++.+.+.+++.
T Consensus 46 tKaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 46 TKAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred hhhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 344566666655220 01113455667999 8999999999999998874
No 196
>PRK06096 molybdenum transport protein ModD; Provisional
Probab=20.76 E-value=6.3e+02 Score=22.79 Aligned_cols=53 Identities=13% Similarity=0.066 Sum_probs=41.4
Q ss_pred ChhHHHHHHhccceEEEecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 022837 141 GATIKSFMDDSQAVIKISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKLS 193 (291)
Q Consensus 141 G~~Ik~I~~~tGa~I~i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l~ 193 (291)
-....++-+..|+++.+.-.+...-...+.+++++|+...+..|++..+.+|+
T Consensus 49 ~~~a~~if~~l~~~v~~~~~dG~~v~~G~~i~~~~G~a~~ll~~eR~alN~l~ 101 (284)
T PRK06096 49 ISVACKMLTTLGLTIDDAVSDGSQANAGQRLISAQGNAAALHQGWKAVQNVLE 101 (284)
T ss_pred HHHHHHHHHHcCCEEEEEeCCCCEeCCCCEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 34567887888998888765554445578999999999999999988877664
No 197
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=20.44 E-value=5.7e+02 Score=22.14 Aligned_cols=133 Identities=13% Similarity=0.079 Sum_probs=72.8
Q ss_pred HHHHHHhCCcEEEcCCCC------CCCCCCceEEEEec-CHHHHHHHHHHHHHHHhhhhccccccCCCCCc---------
Q 022837 58 NDFQSQSGARIQLSRSHE------FFPGTTDRIIMISG-TIDEILRAVDLVIDKLLTELHAEDQADDVGTK--------- 121 (291)
Q Consensus 58 k~I~~~tga~I~v~~~~~------~~p~~~er~v~I~G-~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~--------- 121 (291)
-..-+.+++.|-+.++.. ..+-+.+-.+.|.| ...+|..|++..++.+.+....- -.++....
T Consensus 52 DeA~KAAnVevv~a~~~~gGaghg~~~~~G~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~-~~n~~g~~~~~a~~~aR 130 (217)
T PRK15405 52 DEATKQAMVEVVYARSFYAGAAHASTPLAGEVIGILAGPNPAEVRAGLDAMVAFIENGAAFQ-SANDDDSTAFFAHVVSR 130 (217)
T ss_pred HHHHhhcceEEEEEEeeccccccCCCCCCccEEEEEeCCCHHHHHHHHHHHHHHHHhhhceE-eeCCCCCEEEEEEEccc
Confidence 555667778887765320 01112345688999 89999999999988887653221 01111100
Q ss_pred ----eEEEEEecC-CccceeeccCChhHHHH---HHhccceEE-EecCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 022837 122 ----TKLRLIVPN-SSCGSIIGKAGATIKSF---MDDSQAVIK-ISRLDHSYYGLNDRLVTLTGTLDEQMRALELILLKL 192 (291)
Q Consensus 122 ----~~~~i~VP~-~~vg~IIGk~G~~Ik~I---~~~tGa~I~-i~~~~~~~~~~~er~V~I~G~~~~v~~A~~~I~~~l 192 (291)
....+-+|. +-.|.|||.=+.-+=-+ .....+++. +.... ....-.-..|+|+..+|+.|...-.+.+
T Consensus 131 ag~~l~k~~g~~~G~a~~~li~~P~~~~~~~D~AlKaA~V~~~~~~~P~---~~t~f~~~~ltG~~~A~r~A~~a~~e~v 207 (217)
T PRK15405 131 TGSYLSKTAGIAEGEPLAYLIAPPLEAMYGIDAALKAADVQLVTFVGPP---SETNFGGALLTGSQSACKAACNAFTDAV 207 (217)
T ss_pred HHHHHHHHcCCCCCceeEEEecCcHHHHHHHHHHHhhcCceEEEEeCCC---CCceecCeeEEeCHHHHHHHHHHHHHHH
Confidence 011122332 33467777664433222 222344442 22111 1112222899999999999888877766
Q ss_pred hc
Q 022837 193 SE 194 (291)
Q Consensus 193 ~e 194 (291)
+.
T Consensus 208 ~~ 209 (217)
T PRK15405 208 LE 209 (217)
T ss_pred HH
Confidence 54
Done!