Query 025165
Match_columns 257
No_of_seqs 156 out of 1462
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 03:16:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025165hhsearch_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 6.8E-34 1.5E-38 248.9 21.5 220 17-247 5-237 (402)
2 KOG2192 PolyC-binding hnRNP-K 100.0 5.8E-30 1.3E-34 219.0 12.2 193 10-232 14-207 (390)
3 KOG2193 IGF-II mRNA-binding pr 99.9 9.1E-27 2E-31 209.8 12.0 179 45-240 194-379 (584)
4 KOG2190 PolyC-binding proteins 99.9 4.6E-25 1E-29 208.0 20.9 165 49-221 42-210 (485)
5 KOG1676 K-homology type RNA bi 99.9 3E-25 6.4E-30 207.9 15.3 167 47-224 136-305 (600)
6 KOG1676 K-homology type RNA bi 99.9 7E-23 1.5E-27 192.0 15.4 164 49-224 229-394 (600)
7 KOG2192 PolyC-binding hnRNP-K 99.8 9.4E-20 2E-24 156.5 12.7 162 47-220 120-385 (390)
8 KOG2190 PolyC-binding proteins 99.8 7.1E-19 1.5E-23 166.2 17.6 163 49-221 137-411 (485)
9 TIGR03665 arCOG04150 arCOG0415 99.8 1.1E-18 2.4E-23 144.9 11.0 146 54-228 2-160 (172)
10 KOG2193 IGF-II mRNA-binding pr 99.8 1.9E-18 4.1E-23 156.3 12.8 161 47-224 408-569 (584)
11 PRK13763 putative RNA-processi 99.7 3E-17 6.5E-22 137.3 12.5 148 50-226 3-164 (180)
12 cd02396 PCBP_like_KH K homolog 99.5 4.5E-14 9.8E-19 98.8 7.6 63 145-213 2-64 (65)
13 cd02396 PCBP_like_KH K homolog 99.5 1.2E-13 2.6E-18 96.6 5.8 63 51-118 1-64 (65)
14 cd02394 vigilin_like_KH K homo 99.4 1.7E-12 3.8E-17 89.6 6.0 61 145-214 2-62 (62)
15 PF00013 KH_1: KH domain syndr 99.3 2E-12 4.4E-17 88.7 5.8 60 144-213 1-60 (60)
16 cd02393 PNPase_KH Polynucleoti 99.3 1E-11 2.2E-16 85.8 7.8 57 144-213 3-60 (61)
17 cd00105 KH-I K homology RNA-bi 99.3 2E-11 4.4E-16 84.4 8.2 62 145-213 2-63 (64)
18 PF00013 KH_1: KH domain syndr 99.3 4.5E-12 9.8E-17 87.0 3.6 60 51-118 1-60 (60)
19 cd02394 vigilin_like_KH K homo 99.2 7.6E-12 1.6E-16 86.4 4.3 60 52-118 2-61 (62)
20 KOG2191 RNA-binding protein NO 99.2 6.7E-11 1.5E-15 104.8 10.4 79 141-224 37-116 (402)
21 cd00105 KH-I K homology RNA-bi 99.2 3.3E-11 7.1E-16 83.3 5.9 62 52-118 2-63 (64)
22 COG1094 Predicted RNA-binding 99.2 4E-10 8.6E-15 93.9 13.0 156 49-228 7-173 (194)
23 cd02393 PNPase_KH Polynucleoti 99.1 8.6E-11 1.9E-15 81.1 5.8 58 51-118 3-60 (61)
24 PF13014 KH_3: KH domain 99.1 1E-10 2.2E-15 75.0 4.5 42 60-101 1-43 (43)
25 PF13014 KH_3: KH domain 99.1 2E-10 4.2E-15 73.6 5.5 43 153-201 1-43 (43)
26 smart00322 KH K homology RNA-b 99.0 2.7E-09 5.8E-14 73.6 9.1 66 143-217 3-68 (69)
27 KOG2113 Predicted RNA binding 98.9 1.1E-09 2.4E-14 96.4 4.8 152 48-217 24-181 (394)
28 smart00322 KH K homology RNA-b 98.9 7.8E-09 1.7E-13 71.3 7.3 67 49-122 2-68 (69)
29 KOG2279 Kinase anchor protein 98.8 7.3E-09 1.6E-13 97.3 5.7 146 46-219 64-209 (608)
30 cd02395 SF1_like-KH Splicing f 98.6 1.9E-07 4.1E-12 73.0 8.2 71 151-222 14-98 (120)
31 TIGR03665 arCOG04150 arCOG0415 98.5 1.7E-07 3.7E-12 77.9 5.7 61 147-219 2-65 (172)
32 PRK08406 transcription elongat 98.5 4.7E-07 1E-11 72.8 7.5 103 50-178 32-134 (140)
33 PRK13763 putative RNA-processi 98.5 4E-07 8.6E-12 76.3 7.0 64 144-219 4-71 (180)
34 cd02395 SF1_like-KH Splicing f 98.5 4.5E-07 9.7E-12 70.9 6.5 72 53-126 3-97 (120)
35 KOG2208 Vigilin [Lipid transpo 98.4 1.4E-06 3E-11 87.3 8.8 146 47-221 344-490 (753)
36 KOG2279 Kinase anchor protein 98.3 1.1E-06 2.4E-11 82.9 6.9 162 45-215 135-364 (608)
37 TIGR02696 pppGpp_PNP guanosine 98.3 3.9E-06 8.5E-11 83.0 10.4 94 108-219 548-642 (719)
38 TIGR01952 nusA_arch NusA famil 98.1 1.2E-05 2.6E-10 64.6 8.0 103 51-179 34-136 (141)
39 KOG2208 Vigilin [Lipid transpo 98.1 1.4E-05 3.1E-10 80.2 10.1 164 49-223 200-418 (753)
40 TIGR03591 polynuc_phos polyrib 98.0 1.9E-05 4E-10 78.8 8.5 93 110-219 522-615 (684)
41 COG0195 NusA Transcription elo 97.8 8.9E-05 1.9E-09 62.4 7.4 103 51-180 77-179 (190)
42 PLN00207 polyribonucleotide nu 97.8 8.3E-05 1.8E-09 75.3 8.0 100 108-224 654-755 (891)
43 TIGR02696 pppGpp_PNP guanosine 97.7 4.7E-05 1E-09 75.4 6.1 66 49-124 577-642 (719)
44 KOG0119 Splicing factor 1/bran 97.7 0.00019 4E-09 67.4 8.3 78 142-219 137-230 (554)
45 COG1185 Pnp Polyribonucleotide 97.6 0.00014 3.1E-09 70.9 7.6 100 108-225 521-622 (692)
46 KOG0336 ATP-dependent RNA heli 97.6 0.00015 3.4E-09 67.1 6.6 70 140-219 44-113 (629)
47 TIGR03591 polynuc_phos polyrib 97.4 0.00016 3.6E-09 72.1 5.4 65 49-123 550-614 (684)
48 cd02134 NusA_KH NusA_K homolog 97.4 0.00021 4.6E-09 49.1 4.1 37 49-85 24-60 (61)
49 KOG1588 RNA-binding protein Sa 97.4 0.0035 7.6E-08 54.8 11.8 86 140-225 89-197 (259)
50 PRK12328 nusA transcription el 97.3 0.00069 1.5E-08 62.5 7.4 97 59-183 251-348 (374)
51 TIGR01953 NusA transcription t 97.3 0.00072 1.6E-08 62.0 7.4 94 60-180 244-338 (341)
52 PRK11824 polynucleotide phosph 97.3 0.00051 1.1E-08 68.7 6.7 95 108-219 523-618 (693)
53 KOG0119 Splicing factor 1/bran 97.2 0.00045 9.8E-09 64.9 5.4 72 49-124 137-230 (554)
54 KOG1588 RNA-binding protein Sa 97.2 0.00037 8E-09 60.9 4.4 41 46-86 88-134 (259)
55 KOG2814 Transcription coactiva 97.2 0.00052 1.1E-08 61.7 5.4 71 143-221 57-127 (345)
56 PRK12327 nusA transcription el 97.2 0.00092 2E-08 61.8 7.0 95 60-181 246-341 (362)
57 KOG2814 Transcription coactiva 97.2 0.00043 9.3E-09 62.2 4.1 71 49-125 56-126 (345)
58 KOG2113 Predicted RNA binding 97.1 0.0003 6.5E-09 62.7 2.9 65 141-215 24-88 (394)
59 cd02134 NusA_KH NusA_K homolog 97.0 0.0011 2.5E-08 45.4 4.5 36 143-178 25-60 (61)
60 PRK09202 nusA transcription el 97.0 0.0017 3.7E-08 62.1 7.2 93 61-181 247-340 (470)
61 PRK12329 nusA transcription el 97.0 0.0014 3E-08 61.6 6.2 94 60-180 278-372 (449)
62 PRK04163 exosome complex RNA-b 97.0 0.002 4.4E-08 56.2 6.7 68 144-224 146-214 (235)
63 KOG0336 ATP-dependent RNA heli 97.0 0.001 2.2E-08 61.8 4.6 55 46-103 43-97 (629)
64 PRK00468 hypothetical protein; 96.9 0.0011 2.3E-08 47.6 3.1 34 46-79 26-59 (75)
65 TIGR03319 YmdA_YtgF conserved 96.8 0.0064 1.4E-07 58.9 9.4 65 143-219 204-270 (514)
66 PRK00106 hypothetical protein; 96.8 0.0077 1.7E-07 58.4 9.7 65 143-219 225-291 (535)
67 PRK12704 phosphodiesterase; Pr 96.8 0.0071 1.5E-07 58.6 9.5 65 143-219 210-276 (520)
68 PRK02821 hypothetical protein; 96.8 0.0013 2.8E-08 47.3 3.0 36 46-81 27-62 (77)
69 PF14611 SLS: Mitochondrial in 96.7 0.096 2.1E-06 44.6 14.9 134 53-225 29-171 (210)
70 PLN00207 polyribonucleotide nu 96.7 0.0016 3.5E-08 66.2 4.5 66 49-124 684-750 (891)
71 COG1185 Pnp Polyribonucleotide 96.6 0.0047 1E-07 60.6 6.5 67 49-125 551-617 (692)
72 COG1837 Predicted RNA-binding 96.6 0.0022 4.8E-08 45.9 3.2 32 47-78 27-58 (76)
73 PRK12704 phosphodiesterase; Pr 96.3 0.0091 2E-07 57.9 6.8 51 48-103 208-259 (520)
74 PRK01064 hypothetical protein; 96.3 0.0036 7.9E-08 45.1 3.0 33 47-79 27-59 (78)
75 COG5176 MSL5 Splicing factor ( 96.2 0.01 2.3E-07 50.2 5.4 78 142-219 147-240 (269)
76 COG1094 Predicted RNA-binding 96.1 0.013 2.9E-07 49.2 5.6 53 60-124 112-164 (194)
77 KOG3273 Predicted RNA-binding 96.1 0.016 3.4E-07 48.9 5.9 157 51-226 75-238 (252)
78 PRK02821 hypothetical protein; 96.0 0.0099 2.1E-07 42.8 4.0 30 143-172 31-60 (77)
79 TIGR03319 YmdA_YtgF conserved 96.0 0.013 2.9E-07 56.7 6.0 50 48-102 202-252 (514)
80 KOG1067 Predicted RNA-binding 95.9 0.024 5.1E-07 54.6 6.8 98 109-224 567-665 (760)
81 PRK00106 hypothetical protein; 95.9 0.016 3.5E-07 56.2 5.9 50 48-102 223-273 (535)
82 PRK00468 hypothetical protein; 95.8 0.0096 2.1E-07 42.6 3.3 30 142-171 29-58 (75)
83 PRK04163 exosome complex RNA-b 95.8 0.016 3.4E-07 50.6 5.2 60 52-121 147-206 (235)
84 COG5176 MSL5 Splicing factor ( 95.7 0.02 4.4E-07 48.5 5.2 42 47-88 145-192 (269)
85 PRK11824 polynucleotide phosph 95.6 0.0093 2E-07 59.8 3.2 63 51-123 555-617 (693)
86 PRK12705 hypothetical protein; 95.4 0.05 1.1E-06 52.5 7.3 66 143-220 198-265 (508)
87 COG1837 Predicted RNA-binding 95.4 0.02 4.3E-07 41.0 3.4 30 141-170 28-57 (76)
88 PRK08406 transcription elongat 95.4 0.016 3.4E-07 46.6 3.2 38 49-86 98-135 (140)
89 PF13083 KH_4: KH domain; PDB: 95.3 0.011 2.4E-07 41.8 2.0 36 47-82 26-61 (73)
90 KOG2874 rRNA processing protei 95.3 0.028 6.1E-07 49.6 4.9 51 155-219 161-211 (356)
91 cd02409 KH-II KH-II (K homolo 95.0 0.036 7.8E-07 37.7 3.9 35 49-83 24-58 (68)
92 PRK01064 hypothetical protein; 95.0 0.03 6.6E-07 40.4 3.5 31 141-171 28-58 (78)
93 PF13184 KH_5: NusA-like KH do 95.0 0.022 4.8E-07 40.1 2.6 38 51-88 4-47 (69)
94 KOG4369 RTK signaling protein 94.2 0.023 4.9E-07 58.8 1.6 72 48-124 1338-1410(2131)
95 PRK12705 hypothetical protein; 93.7 0.1 2.2E-06 50.4 5.1 40 49-88 197-237 (508)
96 PF07650 KH_2: KH domain syndr 93.3 0.056 1.2E-06 38.5 1.9 35 50-84 25-59 (78)
97 PF13184 KH_5: NusA-like KH do 93.1 0.092 2E-06 36.9 2.8 37 144-180 4-46 (69)
98 TIGR01952 nusA_arch NusA famil 93.0 0.082 1.8E-06 42.5 2.7 39 48-86 98-136 (141)
99 PRK06418 transcription elongat 93.0 0.13 2.9E-06 42.4 4.0 47 41-88 52-98 (166)
100 KOG4369 RTK signaling protein 93.0 0.046 9.9E-07 56.7 1.5 71 143-219 1340-1410(2131)
101 PF13083 KH_4: KH domain; PDB: 92.8 0.069 1.5E-06 37.6 1.8 32 143-174 29-60 (73)
102 COG1097 RRP4 RNA-binding prote 92.7 0.24 5.1E-06 43.1 5.2 66 145-223 148-214 (239)
103 cd02409 KH-II KH-II (K homolo 92.5 0.23 4.9E-06 33.6 4.1 34 143-176 25-58 (68)
104 cd02414 jag_KH jag_K homology 92.4 0.12 2.7E-06 36.8 2.7 35 51-85 25-59 (77)
105 PF07650 KH_2: KH domain syndr 91.8 0.11 2.5E-06 36.9 1.9 35 143-177 25-59 (78)
106 COG0195 NusA Transcription elo 91.7 0.17 3.7E-06 42.7 3.2 37 51-87 143-179 (190)
107 COG1855 ATPase (PilT family) [ 91.3 0.15 3.3E-06 48.4 2.7 40 49-88 485-524 (604)
108 PRK12328 nusA transcription el 91.0 0.27 5.8E-06 45.7 4.0 41 48-88 306-346 (374)
109 TIGR01953 NusA transcription t 90.7 0.29 6.4E-06 45.0 4.0 40 48-87 299-338 (341)
110 cd02410 archeal_CPSF_KH The ar 90.5 2 4.3E-05 34.6 8.0 95 64-181 20-114 (145)
111 PRK13764 ATPase; Provisional 90.4 0.23 4.9E-06 49.1 3.1 41 48-88 479-519 (602)
112 PRK13764 ATPase; Provisional 89.7 0.57 1.2E-05 46.4 5.2 43 143-185 481-523 (602)
113 cd02413 40S_S3_KH K homology R 89.3 0.37 8.1E-06 34.9 2.8 37 50-86 30-66 (81)
114 cd02414 jag_KH jag_K homology 89.2 0.45 9.7E-06 33.9 3.1 34 144-177 25-58 (77)
115 PRK12327 nusA transcription el 88.9 0.5 1.1E-05 43.9 4.0 42 47-88 300-341 (362)
116 PF14611 SLS: Mitochondrial in 88.7 2.8 6.1E-05 35.5 8.2 66 144-221 27-92 (210)
117 PRK09202 nusA transcription el 88.6 0.41 8.9E-06 46.0 3.3 39 49-87 301-339 (470)
118 KOG3273 Predicted RNA-binding 88.6 0.29 6.3E-06 41.4 2.0 56 58-125 177-232 (252)
119 COG1855 ATPase (PilT family) [ 88.5 0.38 8.3E-06 45.8 2.9 40 143-182 486-525 (604)
120 PRK12329 nusA transcription el 87.2 0.59 1.3E-05 44.3 3.3 41 48-88 333-373 (449)
121 COG1782 Predicted metal-depend 86.9 2.3 4.9E-05 41.1 7.1 97 62-181 41-137 (637)
122 PRK06418 transcription elongat 86.7 0.98 2.1E-05 37.3 4.0 36 144-180 62-97 (166)
123 cd02413 40S_S3_KH K homology R 86.4 1 2.3E-05 32.6 3.6 36 143-178 30-65 (81)
124 cd02412 30S_S3_KH K homology R 86.3 0.69 1.5E-05 35.4 2.8 31 51-81 62-92 (109)
125 cd02411 archeal_30S_S3_KH K ho 85.3 0.85 1.8E-05 33.2 2.7 28 52-79 40-67 (85)
126 cd02410 archeal_CPSF_KH The ar 84.7 1.1 2.4E-05 36.0 3.4 38 53-90 79-116 (145)
127 KOG1067 Predicted RNA-binding 84.7 1.6 3.4E-05 42.6 4.9 67 47-124 594-660 (760)
128 COG1097 RRP4 RNA-binding prote 82.8 1.1 2.5E-05 38.9 2.9 46 53-104 149-194 (239)
129 COG5166 Uncharacterized conser 82.0 1.6 3.5E-05 41.9 3.8 125 63-219 393-524 (657)
130 cd02411 archeal_30S_S3_KH K ho 80.7 2 4.3E-05 31.2 3.2 29 144-172 39-67 (85)
131 COG0092 RpsC Ribosomal protein 80.7 1.3 2.9E-05 38.3 2.6 31 49-79 50-80 (233)
132 cd02412 30S_S3_KH K homology R 80.5 1.8 3.8E-05 33.1 2.9 29 144-172 62-90 (109)
133 COG5166 Uncharacterized conser 79.4 2.3 5.1E-05 40.9 3.9 127 51-179 450-607 (657)
134 TIGR03675 arCOG00543 arCOG0054 79.1 5.9 0.00013 39.6 6.9 97 63-182 36-132 (630)
135 PF08067 ROKNT: ROKNT (NUC014) 79.1 0.78 1.7E-05 28.5 0.4 30 13-47 9-38 (43)
136 KOG2874 rRNA processing protei 77.1 5.2 0.00011 35.7 5.1 26 61-86 160-185 (356)
137 COG0092 RpsC Ribosomal protein 77.1 4.6 0.0001 35.1 4.7 32 143-174 51-86 (233)
138 TIGR00436 era GTP-binding prot 72.3 4.8 0.0001 35.4 3.9 29 143-171 221-250 (270)
139 TIGR00436 era GTP-binding prot 68.4 5.4 0.00012 35.1 3.3 30 50-79 221-251 (270)
140 PRK15494 era GTPase Era; Provi 67.3 6.9 0.00015 35.8 3.9 36 143-178 273-317 (339)
141 COG1159 Era GTPase [General fu 65.5 8.2 0.00018 34.8 3.8 35 144-178 230-273 (298)
142 PRK00089 era GTPase Era; Revie 65.2 8 0.00017 34.2 3.8 36 143-178 226-270 (292)
143 COG1847 Jag Predicted RNA-bind 64.6 3.9 8.4E-05 34.9 1.5 37 49-85 90-126 (208)
144 PRK04191 rps3p 30S ribosomal p 63.9 6.4 0.00014 33.6 2.8 30 52-81 42-71 (207)
145 PRK15494 era GTPase Era; Provi 61.8 8.3 0.00018 35.3 3.3 29 50-78 273-302 (339)
146 COG1782 Predicted metal-depend 61.7 5.8 0.00013 38.4 2.3 38 53-90 102-139 (637)
147 CHL00048 rps3 ribosomal protei 61.3 7.5 0.00016 33.4 2.7 31 50-80 66-96 (214)
148 TIGR01008 rpsC_E_A ribosomal p 60.8 8 0.00017 32.8 2.8 31 50-80 38-68 (195)
149 PRK00089 era GTPase Era; Revie 60.1 9.2 0.0002 33.8 3.2 30 50-79 226-256 (292)
150 COG1702 PhoH Phosphate starvat 59.8 24 0.00051 32.6 5.8 57 149-219 21-79 (348)
151 TIGR03675 arCOG00543 arCOG0054 59.2 7.1 0.00015 39.0 2.5 39 52-90 95-133 (630)
152 PTZ00084 40S ribosomal protein 58.2 9.2 0.0002 33.0 2.8 32 51-82 45-76 (220)
153 COG1159 Era GTPase [General fu 57.2 12 0.00026 33.8 3.3 30 49-78 228-258 (298)
154 PRK04191 rps3p 30S ribosomal p 54.7 14 0.0003 31.6 3.2 28 145-172 42-69 (207)
155 CHL00048 rps3 ribosomal protei 53.1 15 0.00033 31.5 3.3 30 143-172 66-95 (214)
156 TIGR01008 rpsC_E_A ribosomal p 53.1 16 0.00034 31.0 3.3 28 144-171 39-66 (195)
157 PF02749 QRPTase_N: Quinolinat 53.0 41 0.00089 24.3 5.2 54 161-218 32-85 (88)
158 PTZ00084 40S ribosomal protein 50.6 17 0.00037 31.4 3.2 28 144-171 45-72 (220)
159 COG1847 Jag Predicted RNA-bind 50.2 13 0.00029 31.7 2.4 34 144-177 92-125 (208)
160 KOG1423 Ras-like GTPase ERA [C 50.1 14 0.0003 33.8 2.6 32 49-80 327-359 (379)
161 KOG1423 Ras-like GTPase ERA [C 46.6 35 0.00076 31.3 4.6 34 140-173 325-359 (379)
162 TIGR01009 rpsC_bact ribosomal 45.9 19 0.00042 30.8 2.8 28 52-79 64-91 (211)
163 PF09869 DUF2096: Uncharacteri 41.3 97 0.0021 25.6 6.0 59 140-218 110-168 (169)
164 TIGR01009 rpsC_bact ribosomal 39.2 32 0.0007 29.5 3.1 28 144-171 63-90 (211)
165 COG2101 SPT15 TATA-box binding 37.7 79 0.0017 26.4 5.0 26 195-220 155-182 (185)
166 COG4010 Uncharacterized protei 37.1 1.2E+02 0.0027 24.5 5.8 44 163-219 126-169 (170)
167 PRK00310 rpsC 30S ribosomal pr 36.4 33 0.00072 29.8 2.8 30 51-80 63-92 (232)
168 PRK15468 carboxysome structura 34.3 1.1E+02 0.0024 23.4 5.0 41 170-221 61-101 (111)
169 PF10369 ALS_ss_C: Small subun 33.0 1.3E+02 0.0028 21.1 5.0 41 162-213 16-56 (75)
170 PRK00310 rpsC 30S ribosomal pr 28.4 58 0.0013 28.3 3.0 29 144-172 63-91 (232)
171 PRK04021 hypothetical protein; 27.4 1.7E+02 0.0036 21.6 4.9 39 164-210 51-90 (92)
172 PF02080 TrkA_C: TrkA-C domain 26.1 73 0.0016 21.3 2.6 52 162-213 14-70 (71)
173 TIGR01334 modD putative molybd 25.0 3.2E+02 0.0069 24.4 7.1 56 160-219 46-101 (277)
174 PF00936 BMC: BMC domain; Int 24.0 1.4E+02 0.003 20.9 3.8 28 193-220 38-65 (75)
175 cd07046 BMC_PduU-EutS 1,2-prop 23.5 1.5E+02 0.0032 22.8 4.1 29 194-222 73-101 (110)
176 TIGR03802 Asp_Ala_antiprt aspa 23.3 4.4E+02 0.0094 26.0 8.4 68 144-217 304-380 (562)
177 PRK05848 nicotinate-nucleotide 22.5 3.7E+02 0.008 23.9 7.1 56 160-219 44-99 (273)
178 PF00352 TBP: Transcription fa 20.7 1.8E+02 0.004 20.7 4.0 36 172-220 48-85 (86)
179 PF09383 NIL: NIL domain; Int 20.5 2.5E+02 0.0054 19.2 4.6 53 160-215 14-68 (76)
180 PF03946 Ribosomal_L11_N: Ribo 20.2 85 0.0018 21.2 2.0 29 52-80 2-36 (60)
181 KOG3429 Predicted peptidyl-tRN 20.1 80 0.0017 26.0 2.1 61 65-125 50-126 (172)
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=6.8e-34 Score=248.92 Aligned_cols=220 Identities=25% Similarity=0.378 Sum_probs=169.7
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCcccc-CCCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc---ccCC
Q 025165 17 TEPEPRHDVSGKRRREDGEIEGSDPKRR-AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARH 92 (257)
Q Consensus 17 ~~~~~~~~~~~kr~~e~~~~~~~~~~~~-~~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~---~~~~ 92 (257)
++-..+..+++||+++...+........ .....+++|||||+..+|.||||||++|.+||++|||+|++++. .|++
T Consensus 5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT 84 (402)
T KOG2191|consen 5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT 84 (402)
T ss_pred CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence 4455667788899999877543322222 22345999999999999999999999999999999999999954 6889
Q ss_pred CccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhh--ccCCCcceEEEEEeccCccceeecCCChhHHHHHH
Q 025165 93 EERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKV--AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170 (257)
Q Consensus 93 ~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~--~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~ 170 (257)
+||+|+|+|+- ..+......|.++|++..........+ .........++++||++.+|.||||+|++||.|++
T Consensus 85 TeRvcli~Gt~-----eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~E 159 (402)
T KOG2191|consen 85 TERVCLIQGTV-----EALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQE 159 (402)
T ss_pred cceEEEEeccH-----HHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHH
Confidence 99999999994 356666677778877654322110000 01123345689999999999999999999999999
Q ss_pred HhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCc---ccC----CCCCCCCCCCCCCCC
Q 025165 171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV---ISI----SPAYNYSAIRPAQPF 243 (257)
Q Consensus 171 ~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~---~~~----~p~~~~~~~~~~~~~ 243 (257)
++||+|+|++.+ |... ...+|+|++.|++++..+|+.+|+++|.|+|+..+ .+| .|..|+++ +|++|
T Consensus 160 qsga~iqisPqk--pt~~--sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnP--tGspy 233 (402)
T KOG2191|consen 160 QSGAWIQISPQK--PTGI--SLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNP--TGSPY 233 (402)
T ss_pred hhCcceEecccC--CCCc--cceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCC--CCCCC
Confidence 999999998522 2222 36899999999999999999999999999999865 244 58999988 66666
Q ss_pred cCCC
Q 025165 244 VEPT 247 (257)
Q Consensus 244 ~~~~ 247 (257)
.-+.
T Consensus 234 a~~~ 237 (402)
T KOG2191|consen 234 AYQA 237 (402)
T ss_pred CCCC
Confidence 6543
No 2
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=5.8e-30 Score=219.00 Aligned_cols=193 Identities=28% Similarity=0.433 Sum_probs=161.0
Q ss_pred cCCCCCCCCCCCCCCCCCCccCCCCCCCCCCccccCCCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccc
Q 025165 10 NPTVSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI 89 (257)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~kr~~e~~~~~~~~~~~~~~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~ 89 (257)
++-|..++++.++.+..+||+.+|+.. +++++. .+.+|||+.+..+|+||||+|++||+|+.+++|+|+|+++
T Consensus 14 t~q~~~~~~~~e~g~~~gkrp~~d~~~---qa~k~~---r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds- 86 (390)
T KOG2192|consen 14 TEQPEETFPNTETGGEFGKRPAEDMEE---QAFKRS---RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS- 86 (390)
T ss_pred CCChhhcCCCCcccccccCCcchhhHH---HHhhhc---ceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-
Confidence 556677899999999999999999873 333333 4899999999999999999999999999999999999988
Q ss_pred cCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHH
Q 025165 90 ARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLR 169 (257)
Q Consensus 90 ~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~ 169 (257)
+++||+|+|+...+ .+-+-+..|.-.+.+.- ...+.+.++++|+.+++|.|||++|++||+|+
T Consensus 87 -~~peri~tisad~~-----ti~~ilk~iip~lee~f-----------~~~~pce~rllihqs~ag~iigrngskikelr 149 (390)
T KOG2192|consen 87 -SGPERILTISADIE-----TIGEILKKIIPTLEEGF-----------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELR 149 (390)
T ss_pred -CCCceeEEEeccHH-----HHHHHHHHHhhhhhhCC-----------CCCCchhhhhhhhhhhccceecccchhHHHHH
Confidence 48999999999743 34444444444443321 12245789999999999999999999999999
Q ss_pred HHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCCCcc-cCCCCC
Q 025165 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVI-SISPAY 232 (257)
Q Consensus 170 ~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~-~~~p~~ 232 (257)
+++.|+++|+. .||. ++++|+|.|.|.+.+|..++++|+++|.|.|.+++. +|+|.|
T Consensus 150 ekcsarlkift-----~c~p-~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~f 207 (390)
T KOG2192|consen 150 EKCSARLKIFT-----ECCP-HSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNF 207 (390)
T ss_pred Hhhhhhhhhhh-----ccCC-CCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccc
Confidence 99999999984 4543 799999999999999999999999999999999885 665554
No 3
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=9.1e-27 Score=209.75 Aligned_cols=179 Identities=26% Similarity=0.462 Sum_probs=154.5
Q ss_pred CCCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc-ccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHh
Q 025165 45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (257)
Q Consensus 45 ~~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~ 123 (257)
...-++.+|+|||..++|.||||.|+|||.|.+.|.|+|+|.+. +.|..|++++|-+++| .+.+|+.+|+++|.
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpE-----g~s~Ac~~ILeimq 268 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPE-----GTSKACKMILEIMQ 268 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCcc-----chHHHHHHHHHHHH
Confidence 33568899999999999999999999999999999999999854 4578899999999987 56799999999997
Q ss_pred cCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025165 124 KDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
.+.....-. ..+.++++.++.+||+||||.|++||+|.++||++|.|.+-.++.. .+.+|.+++.|+.
T Consensus 269 kEA~~~k~~--------~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~----ynpERTItVkGsi 336 (584)
T KOG2193|consen 269 KEAVDDKVA--------EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL----YNPERTITVKGSI 336 (584)
T ss_pred Hhhhccchh--------hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc----cCccceEEecccH
Confidence 664432221 2357899999999999999999999999999999999988666655 3789999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCcccC------CCCCCCCCCCCC
Q 025165 204 PAVLNALVEIGNQLRENPPRQVISI------SPAYNYSAIRPA 240 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~~~~~~------~p~~~~~~~~~~ 240 (257)
++|..|..+|+.+|+|.++++..++ .|++|....+++
T Consensus 337 Eac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f 379 (584)
T KOG2193|consen 337 EACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLF 379 (584)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCC
Confidence 9999999999999999999986533 688988887665
No 4
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=4.6e-25 Score=207.98 Aligned_cols=165 Identities=33% Similarity=0.558 Sum_probs=131.6
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC---
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD--- 125 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~--- 125 (257)
..++|+||+...+|.||||+|.+||+||+++.++|+|.+..+++.||+++|+|...+...+.+.+|+..+++.+...
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence 33489999999999999999999999999999999999998899999999999221112334555665555555432
Q ss_pred -CCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHH
Q 025165 126 -DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP 204 (257)
Q Consensus 126 -~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~ 204 (257)
+....+.... ......+++|+||.+++|+||||+|+.||+|+++|||+|.+.+. .+|. .++|.|+|.|.++
T Consensus 122 d~~~~~d~~~~--~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~-----ster~V~IsG~~~ 193 (485)
T KOG2190|consen 122 DDEAAEDNGED--ASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN-----STERAVTISGEPD 193 (485)
T ss_pred cccccccCCcc--ccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc-----ccceeEEEcCchH
Confidence 2111111100 01114689999999999999999999999999999999999754 8887 5789999999999
Q ss_pred HHHHHHHHHHHHHhcCC
Q 025165 205 AVLNALVEIGNQLRENP 221 (257)
Q Consensus 205 ~v~~A~~~I~~~l~e~~ 221 (257)
+|.+|+..|..+|++++
T Consensus 194 av~~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 194 AVKKALVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999999953
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.93 E-value=3e-25 Score=207.86 Aligned_cols=167 Identities=23% Similarity=0.377 Sum_probs=137.7
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccc--cCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAI--ARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~--~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
..+++..|+||.+.+|+||||+|++||+|++.+||++.+.... ..+..+-+.|+|.++ .++.|..+++++|.+
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~-----~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPD-----KVEQAKQLVADILRE 210 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHH-----HHHHHHHHHHHHHHh
Confidence 4568999999999999999999999999999999999987442 123678899999975 789999999999987
Q ss_pred CCCCCchhhh-hccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025165 125 DDDSNSEASK-VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 125 ~~~~~~~~~~-~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
+.....-... ...+.....+.++.||++.||.||||+|++||+|+.+||++|+|.+ |+.|. +.+|.+.|.|+.
T Consensus 211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p~-----speR~~~IiG~~ 284 (600)
T KOG1676|consen 211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDPS-----SPERPAQIIGTV 284 (600)
T ss_pred cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCCC-----CccceeeeecCH
Confidence 5443322211 1111223448999999999999999999999999999999999865 45554 789999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCC
Q 025165 204 PAVLNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~~ 224 (257)
+.|++|.++|.++|.+.....
T Consensus 285 d~ie~Aa~lI~eii~~~~~~~ 305 (600)
T KOG1676|consen 285 DQIEHAAELINEIIAEAEAGA 305 (600)
T ss_pred HHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999977663
No 6
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.90 E-value=7e-23 Score=192.01 Aligned_cols=164 Identities=23% Similarity=0.352 Sum_probs=132.4
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEc-ccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCC
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~-~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~ 127 (257)
...+++.||.+.||.||||+|++||+|+.+||+||+|- +..+.+.||.+.|.|+.+ .+..|.++|.++|.+...
T Consensus 229 ~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d-----~ie~Aa~lI~eii~~~~~ 303 (600)
T KOG1676|consen 229 SATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVD-----QIEHAAELINEIIAEAEA 303 (600)
T ss_pred cceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHH-----HHHHHHHHHHHHHHHHhc
Confidence 45899999999999999999999999999999999997 445578999999999964 677888888888866433
Q ss_pred CCchhhhhccCCC-cceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHH
Q 025165 128 SNSEASKVAAGHV-AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (257)
Q Consensus 128 ~~~~~~~~~~~~~-~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v 206 (257)
...... ..+.. ..-.+.+.||.+.||.||||+|++||.|..+|||++.+.+. -|.. +..+|+|+|.|+..+|
T Consensus 304 ~~~~~~--~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~--~p~~---~~~ektf~IrG~~~QI 376 (600)
T KOG1676|consen 304 GAGGGM--GGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ--PPNG---NPKEKTFVIRGDKRQI 376 (600)
T ss_pred cCCCCc--CCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC--CCCC---CccceEEEEecCcccc
Confidence 211000 00111 11268999999999999999999999999999999998654 2321 3679999999999999
Q ss_pred HHHHHHHHHHHhcCCCCC
Q 025165 207 LNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 207 ~~A~~~I~~~l~e~~~~~ 224 (257)
..|..||..++.+.....
T Consensus 377 dhAk~LIr~kvg~~~~n~ 394 (600)
T KOG1676|consen 377 DHAKQLIRDKVGDIAPNT 394 (600)
T ss_pred hHHHHHHHHHhcccCCCC
Confidence 999999999999955443
No 7
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.82 E-value=9.4e-20 Score=156.45 Aligned_cols=162 Identities=27% Similarity=0.452 Sum_probs=131.4
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEc-ccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA-DAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~-~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
.+...+||||..+.+|.|||++|+.||.||+++.++++|- ...|++++|||.+.|.+. .+..+++.|++.|.+.
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k-----~v~~~i~~il~~i~e~ 194 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPK-----RVVECIKIILDLISES 194 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcc-----hHHHHHHHHHHHhhcC
Confidence 4678899999999999999999999999999999999986 556789999999999876 5778888888888763
Q ss_pred CCC-------------Cchh------------------------------------------------------------
Q 025165 126 DDS-------------NSEA------------------------------------------------------------ 132 (257)
Q Consensus 126 ~~~-------------~~~~------------------------------------------------------------ 132 (257)
... ..+.
T Consensus 195 pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~s 274 (390)
T KOG2192|consen 195 PIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPS 274 (390)
T ss_pred CcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCC
Confidence 210 0000
Q ss_pred ----h-----hh-------------ccC--------CCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025165 133 ----S-----KV-------------AAG--------HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (257)
Q Consensus 133 ----~-----~~-------------~~~--------~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (257)
+ .. +++ ..-..+.++.||.++-|.||||+|.+|++|+.++||.|++...
T Consensus 275 aidtw~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep- 353 (390)
T KOG2192|consen 275 AIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP- 353 (390)
T ss_pred cCCCcCccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc-
Confidence 0 00 000 0124578999999999999999999999999999999998532
Q ss_pred CCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025165 183 QLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 183 ~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~ 220 (257)
+. ++.+|+++|+|+.++++.|.+++...++..
T Consensus 354 -le-----GsedrIitItGTqdQIqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 354 -LE-----GSEDRIITITGTQDQIQNAQYLLQNSVKQY 385 (390)
T ss_pred -CC-----CCCceEEEEeccHHHHhhHHHHHHHHHHhh
Confidence 21 478999999999999999999999999853
No 8
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.81 E-value=7.1e-19 Score=166.18 Aligned_cols=163 Identities=33% Similarity=0.536 Sum_probs=132.9
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc-ccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCC-
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD- 126 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~- 126 (257)
+.++||+||++++|.||||+|+.||+|+++|||+|++... .|.+++|.|+|.|.++ ++.+|+..|...|.+..
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~-----av~~al~~Is~~L~~~~~ 211 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPD-----AVKKALVQISSRLLENPP 211 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchH-----HHHHHHHHHHHHHHhcCC
Confidence 6899999999999999999999999999999999999865 7889999999999965 78999999999997731
Q ss_pred ---C---------C-----------Cch------------------------hhhhc-----------------------
Q 025165 127 ---D---------S-----------NSE------------------------ASKVA----------------------- 136 (257)
Q Consensus 127 ---~---------~-----------~~~------------------------~~~~~----------------------- 136 (257)
. . ..- ..+..
T Consensus 212 ~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v 291 (485)
T KOG2190|consen 212 RSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISV 291 (485)
T ss_pred cCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEe
Confidence 0 0 000 00000
Q ss_pred ----cC-----------C-------------------------CcceEEEEEeccCccceeecCCChhHHHHHHHhCCeE
Q 025165 137 ----AG-----------H-------------------------VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI 176 (257)
Q Consensus 137 ----~~-----------~-------------------------~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I 176 (257)
.. . ...++.+++||++++|+||||+|++|.+||+.|||.|
T Consensus 292 ~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I 371 (485)
T KOG2190|consen 292 GDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASI 371 (485)
T ss_pred ccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCce
Confidence 00 0 1226789999999999999999999999999999999
Q ss_pred EEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025165 177 VILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 177 ~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~ 221 (257)
.|..+++... ..++.++|+|...+...|.+++...+....
T Consensus 372 ~I~~~~~~~~-----~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~ 411 (485)
T KOG2190|consen 372 SILNKEEVSG-----VREALVQITGMLREDLLAQYLIRARLSAPK 411 (485)
T ss_pred EEccccccCC-----cceeEEEecchhHHHHhhhhhcccccccCc
Confidence 9987765422 679999999999999999999966665533
No 9
>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=99.78 E-value=1.1e-18 Score=144.90 Aligned_cols=146 Identities=21% Similarity=0.275 Sum_probs=109.5
Q ss_pred EEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEe---cCCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025165 54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 54 ilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I---~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~ 130 (257)
|.||.+.+|.|||++|++|+.|+++||++|++.+. +..|.| ++. ..++.+|..+|..+.......
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d-----~~~i~kA~~~I~~i~~gf~~e-- 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDED-----PLAVMKAREVVKAIGRGFSPE-- 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCC-----HHHHHHHHHHHHHHHcCCCHH--
Confidence 56899999999999999999999999999999953 356778 333 347888888888876642211
Q ss_pred hhhhhccCCCcceEE-EEEecc---------CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE
Q 025165 131 EASKVAAGHVAANTI-RLLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS 200 (257)
Q Consensus 131 ~~~~~~~~~~~~~~~-~l~Vp~---------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~ 200 (257)
+..+.. + ..+.. -+-|+. ..+|+|||++|++++.|++.|||+|.|. ++.|.|.
T Consensus 70 ~A~~l~-g--d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~ 132 (172)
T TIGR03665 70 KALKLL-D--DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGII 132 (172)
T ss_pred HHHHhc-C--CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEE
Confidence 000000 0 01111 122332 3689999999999999999999999983 2679999
Q ss_pred cCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025165 201 GDVPAVLNALVEIGNQLRENPPRQVISI 228 (257)
Q Consensus 201 G~~~~v~~A~~~I~~~l~e~~~~~~~~~ 228 (257)
|++++++.|.++|.+++.+.++...+.+
T Consensus 133 G~~~~~~~A~~~i~~li~~~~~~~vy~~ 160 (172)
T TIGR03665 133 GDPEQVQIAREAIEMLIEGAPHGTVYKF 160 (172)
T ss_pred CCHHHHHHHHHHHHHHHcCCCChhHHHH
Confidence 9999999999999999988877665443
No 10
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.78 E-value=1.9e-18 Score=156.29 Aligned_cols=161 Identities=25% Similarity=0.383 Sum_probs=135.9
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc-ccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
+..-.+++.||...+|+||||+|.+||+|-..+||.|+|... .+...+|.|+|+|+++ ...+|-..|+.+|.++
T Consensus 408 pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppe-----aqfKAQgrifgKikEe 482 (584)
T KOG2193|consen 408 PEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPE-----AQFKAQGRIFGKIKEE 482 (584)
T ss_pred cchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChH-----HHHhhhhhhhhhhhhh
Confidence 345678999999999999999999999999999999999854 5678899999999976 5678889999999877
Q ss_pred CCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHH
Q 025165 126 DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (257)
Q Consensus 126 ~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~ 205 (257)
.......+ ......+-||.+.+|+||||||.++++|+.-|+|.+.|+ +|+-|+ ..+.-+|.|+|...+
T Consensus 483 nf~~Pkee-------vklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vP-rdqtpd----End~vivriiGhfya 550 (584)
T KOG2193|consen 483 NFFLPKEE-------VKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVP-RDQTPD----ENDQVIVRIIGHFYA 550 (584)
T ss_pred ccCCchhh-------heeeeeeeccchhhhhhhccccccHHHHhccccceEEcc-ccCCCC----ccceeeeeeechhhc
Confidence 55443221 224678999999999999999999999999999999985 455555 266789999999999
Q ss_pred HHHHHHHHHHHHhcCCCCC
Q 025165 206 VLNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 206 v~~A~~~I~~~l~e~~~~~ 224 (257)
.+.|...|.++|.+....+
T Consensus 551 tq~aQrki~~iv~qvkq~~ 569 (584)
T KOG2193|consen 551 TQNAQRKIAHIVNQVKQSG 569 (584)
T ss_pred chHHHHHHHHHHHHHHHhh
Confidence 9999999999999866554
No 11
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.74 E-value=3e-17 Score=137.28 Aligned_cols=148 Identities=21% Similarity=0.280 Sum_probs=110.1
Q ss_pred eEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEec----CCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIIS----SKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~----G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
....+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|. +. ..++.+|..+|..+....
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d-----~~~i~kA~~~I~ai~~gf 72 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGED-----PLAVLKARDIVKAIGRGF 72 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCC-----HHHHHHHHHHHHHHhcCC
Confidence 467899999999999999999999999999999999954 3567775 33 347888999888887642
Q ss_pred CCCCchhhhhccCCCcceEEEE-Ee----c-----cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCce
Q 025165 126 DDSNSEASKVAAGHVAANTIRL-LI----A-----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDR 195 (257)
Q Consensus 126 ~~~~~~~~~~~~~~~~~~~~~l-~V----p-----~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r 195 (257)
... +..+.. + ..+..++ -+ . ...+|+|||++|++++.|++.|||+|.|. ++
T Consensus 73 ~~e--~A~~l~-g--d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~--------------~~ 133 (180)
T PRK13763 73 SPE--KALRLL-D--DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVY--------------GK 133 (180)
T ss_pred CHH--HHHHHh-C--CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEc--------------CC
Confidence 211 000000 0 0011111 11 1 13689999999999999999999999984 13
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHhcCCCCCcc
Q 025165 196 VVQISGDVPAVLNALVEIGNQLRENPPRQVI 226 (257)
Q Consensus 196 ~V~I~G~~~~v~~A~~~I~~~l~e~~~~~~~ 226 (257)
.|.|.|+++++..|...|..+++...+...+
T Consensus 134 ~v~i~G~~~~~~~A~~~I~~li~g~~~~~~~ 164 (180)
T PRK13763 134 TVAIIGDPEQVEIAREAIEMLIEGAPHGTVY 164 (180)
T ss_pred EEEEEeCHHHHHHHHHHHHHHHcCCCcHHHH
Confidence 4999999999999999999999877665433
No 12
>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=99.52 E-value=4.5e-14 Score=98.77 Aligned_cols=63 Identities=43% Similarity=0.652 Sum_probs=56.8
Q ss_pred EEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025165 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
++++||.+.+|+|||++|++|++|+++|||+|.+.+... +. ..+|+|+|+|+++++.+|+.+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~~-----~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-PG-----STERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-CC-----CCceEEEEEeCHHHHHHHHHhh
Confidence 689999999999999999999999999999999965432 22 6789999999999999999987
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=99.46 E-value=1.2e-13 Score=96.58 Aligned_cols=63 Identities=43% Similarity=0.679 Sum_probs=56.1
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEccccc-CCCccEEEecCCCCCchhhHHHHHHHHH
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~-~~~ervv~I~G~~~~~~~~~~~~a~~~I 118 (257)
++||+||.+.+|+||||+|++|++|+++|||+|++.+... +..+|+|+|.|+.+ ++.+|+.+|
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 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPS-----AVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHH-----HHHHHHHhh
Confidence 3799999999999999999999999999999999997643 67899999999954 678888776
No 14
>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=99.35 E-value=1.7e-12 Score=89.65 Aligned_cols=61 Identities=26% Similarity=0.332 Sum_probs=54.6
Q ss_pred EEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH
Q 025165 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG 214 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~ 214 (257)
.++.||.+++++|||++|++|++|+++|||+|.+++.. +.++.|+|+|+.++|.+|..+|+
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 57899999999999999999999999999999996432 35789999999999999998873
No 15
>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=99.34 E-value=2e-12 Score=88.74 Aligned_cols=60 Identities=32% Similarity=0.445 Sum_probs=53.7
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
|.++.||.+++|+|||++|++|++|+++|||+|.|... +....|+|+|++++|++|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~----------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD----------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST----------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC----------CCcEEEEEEeCHHHHHHHHhhC
Confidence 47899999999999999999999999999999999642 1245999999999999999886
No 16
>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=99.31 E-value=1e-11 Score=85.80 Aligned_cols=57 Identities=26% Similarity=0.278 Sum_probs=51.8
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHH
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI 213 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I 213 (257)
...+.||.+++|+|||++|++|++|+++|||+|.+. .++.|.|+|+ +++++.|.++|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~-------------~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE-------------DDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeC-------------CCCEEEEEeCCHHHHHHHHHHh
Confidence 568899999999999999999999999999999984 2467999998 89999999887
No 17
>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=99.28 E-value=2e-11 Score=84.36 Aligned_cols=62 Identities=34% Similarity=0.500 Sum_probs=55.2
Q ss_pred EEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025165 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
.++.||.+++++|||++|++|++|+++|||+|.|..... ...++.|+|.|+.+++..|..+|
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 579999999999999999999999999999999965322 15689999999999999998876
No 18
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.25 E-value=4.5e-12 Score=86.98 Aligned_cols=60 Identities=40% Similarity=0.609 Sum_probs=51.4
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHH
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I 118 (257)
|++|.||.+.+|+|||++|++|++|+++|||+|+|++. + .+..|+|+|+++ .+.+|+++|
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-ERDIVTISGSPE-----QVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHH-----HHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHH-----HHHHHHhhC
Confidence 57899999999999999999999999999999999876 2 455899999643 677777654
No 19
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.24 E-value=7.6e-12 Score=86.43 Aligned_cols=60 Identities=30% Similarity=0.450 Sum_probs=52.0
Q ss_pred EEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHH
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I 118 (257)
.+|.||.+.++.|||++|++|++|+++|||+|.|++.. ..++.|+|+|+++ ++.+|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~-----~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKE-----NVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHH-----HHHHHHHHh
Confidence 57899999999999999999999999999999999763 6789999999953 566666554
No 20
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.22 E-value=6.7e-11 Score=104.79 Aligned_cols=79 Identities=30% Similarity=0.479 Sum_probs=71.6
Q ss_pred cceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCC-CCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ-LPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~-~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
..+.++++||+..+|.||||+|++|.+||.+|||+|++.+..+ .|. .+||+|.|+|+.+++..-.+.|.++|+|
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKire 111 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKIRE 111 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence 3478999999999999999999999999999999999987544 564 8999999999999999999999999999
Q ss_pred CCCCC
Q 025165 220 NPPRQ 224 (257)
Q Consensus 220 ~~~~~ 224 (257)
.++..
T Consensus 112 ~p~~~ 116 (402)
T KOG2191|consen 112 KPQAV 116 (402)
T ss_pred hHHhh
Confidence 87664
No 21
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.20 E-value=3.3e-11 Score=83.33 Aligned_cols=62 Identities=44% Similarity=0.669 Sum_probs=53.2
Q ss_pred EEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHH
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I 118 (257)
.+|.||.+.++.|||++|++|++|+++|||+|.|++......++.|.|.|..+ .+.+|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~-----~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPE-----AVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHH-----HHHHHHHHh
Confidence 68999999999999999999999999999999999765456789999999843 566666554
No 22
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.19 E-value=4e-10 Score=93.86 Aligned_cols=156 Identities=19% Similarity=0.223 Sum_probs=111.6
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCC
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS 128 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~ 128 (257)
.....+.||.+.++-+||+.|++.+.|.+.+++++.++ +.+..|.|.............+|...|..+-..+...
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe 81 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 34567999999999999999999999999999999999 4467788866632111335566666665544333211
Q ss_pred CchhhhhccCCCcceEEE------EEe-c----cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEE
Q 025165 129 NSEASKVAAGHVAANTIR------LLI-A----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV 197 (257)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~------l~V-p----~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V 197 (257)
. ..+.- .+...+. +.- + ....|+|||++|.+.+.|++-|||+|.|. ...|
T Consensus 82 ~--A~~LL---~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV 142 (194)
T COG1094 82 K--ALKLL---EDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV 142 (194)
T ss_pred H--HHHHh---cCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence 0 00000 0000111 011 1 12459999999999999999999999995 3679
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcCCCCCcccC
Q 025165 198 QISGDVPAVLNALVEIGNQLRENPPRQVISI 228 (257)
Q Consensus 198 ~I~G~~~~v~~A~~~I~~~l~e~~~~~~~~~ 228 (257)
.|.|.++++..|.+.|.+++...+++-++.|
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~~h~~Vy~f 173 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGAPHGKVYKF 173 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCCCchhHHHH
Confidence 9999999999999999999999998876543
No 23
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.15 E-value=8.6e-11 Score=81.12 Aligned_cols=58 Identities=36% Similarity=0.542 Sum_probs=47.9
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHH
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I 118 (257)
...|.||.+.+|+||||+|++|++|+++|||+|++++ ++.|.|+|... .++++|..+|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~----~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDK----EAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCH----HHHHHHHHHh
Confidence 5678999999999999999999999999999999986 35799999732 2455565544
No 24
>PF13014 KH_3: KH domain
Probab=99.11 E-value=1e-10 Score=75.00 Aligned_cols=42 Identities=43% Similarity=0.673 Sum_probs=38.2
Q ss_pred ccccccccCchhHHHHHhhhCceEEEcc-cccCCCccEEEecC
Q 025165 60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS 101 (257)
Q Consensus 60 ~vg~IIGkgG~~Ik~I~~~tga~I~i~~-~~~~~~ervv~I~G 101 (257)
+||+||||+|++|++|+++|||+|+|++ ..++..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 4899999999999999999999999998 45567899999987
No 25
>PF13014 KH_3: KH domain
Probab=99.10 E-value=2e-10 Score=73.64 Aligned_cols=43 Identities=37% Similarity=0.652 Sum_probs=37.2
Q ss_pred ccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc
Q 025165 153 QAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG 201 (257)
Q Consensus 153 ~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G 201 (257)
+||+|||++|++|++|+++|||+|+|++ +..+ ++.++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~-----~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP-----GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC-----CCCceEEEEEC
Confidence 5799999999999999999999999976 3333 37899999998
No 26
>smart00322 KH K homology RNA-binding domain.
Probab=99.02 E-value=2.7e-09 Score=73.62 Aligned_cols=66 Identities=33% Similarity=0.462 Sum_probs=58.6
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l 217 (257)
.+.++.||...++++||++|++|++|++.||++|.+.... .....|+|.|..+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~---------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG---------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC---------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4688999999999999999999999999999999985321 24688999999999999999998876
No 27
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.92 E-value=1.1e-09 Score=96.45 Aligned_cols=152 Identities=21% Similarity=0.300 Sum_probs=112.3
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHH---Hhc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL---ILK 124 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~---i~~ 124 (257)
++++..+-||+..++.|.|++|.+||.|+.+|..+|+-+.. ..|.++.++|..+ +|..|.+.|... +.-
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~e-----dv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRHE-----DVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCch-----hHHHHhhcCccccceeee
Confidence 67889999999999999999999999999999999998865 4568899999976 466666655541 110
Q ss_pred CCCCCchhhh-hccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025165 125 DDDSNSEASK-VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 125 ~~~~~~~~~~-~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
.......... ......+..+...-+|...+|.|.|..|++|+.|++.+...|..+-+ ..+.++.++|-+
T Consensus 96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----------~~~~Vf~Vtg~~ 165 (394)
T KOG2113|consen 96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----------CGEPVFCVTGAP 165 (394)
T ss_pred eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc----------CCCceEEEecCC
Confidence 0000000000 00112456678889999999999999999999999999999987533 357899999998
Q ss_pred HH-HHHHH-HHHHHHH
Q 025165 204 PA-VLNAL-VEIGNQL 217 (257)
Q Consensus 204 ~~-v~~A~-~~I~~~l 217 (257)
.+ +++|. ++|...+
T Consensus 166 ~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 166 KNCVKRARSCEIEQTA 181 (394)
T ss_pred cchhhhccccchhhhh
Confidence 88 45555 4554443
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=98.89 E-value=7.8e-09 Score=71.26 Aligned_cols=67 Identities=34% Similarity=0.586 Sum_probs=55.7
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHH
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALI 122 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i 122 (257)
....++.||...+|.+||++|++|++|++.||++|.+.... .....+.|.|..+ ++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~--~~~~~v~i~g~~~-----~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG--SEERVVEITGPPE-----NVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC--CCccEEEEEcCHH-----HHHHHHHHHHHHh
Confidence 35789999999999999999999999999999999998542 2578899999843 5677777776654
No 29
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.79 E-value=7.3e-09 Score=97.35 Aligned_cols=146 Identities=25% Similarity=0.369 Sum_probs=116.6
Q ss_pred CCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
...++.+++.|+...+-.||||+|.+|+.|++.++++|.+.+.. -.++++.++.|-+. .+..|...+++++.+.
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~-----~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPV-----QVCKAKAAIHQILTEN 137 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC-----CCChHHHHHHHHHhcC
Confidence 34678999999999999999999999999999999999998542 25677777776543 4556666667766543
Q ss_pred CCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHH
Q 025165 126 DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (257)
Q Consensus 126 ~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~ 205 (257)
. .+...+-+|...+++++|++|.++.+|+.-++++|.+-.. . . ....+...|.|....
T Consensus 138 ~---------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--g-r----~g~~~~~~i~~qqk~ 195 (608)
T KOG2279|consen 138 T---------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--G-R----LGLSRLIKISGQQKE 195 (608)
T ss_pred C---------------cccccccchhhhcccccccchhhhcchhcccccccccccc--c-c----cccccceecccccch
Confidence 2 1356788999999999999999999999999999998422 1 1 145788888888888
Q ss_pred HHHHHHHHHHHHhc
Q 025165 206 VLNALVEIGNQLRE 219 (257)
Q Consensus 206 v~~A~~~I~~~l~e 219 (257)
++.|..++.+.+.+
T Consensus 196 ~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 196 VAAAKHLILEKVSE 209 (608)
T ss_pred HHHHHhhhhccccc
Confidence 88999999888877
No 30
>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=98.62 E-value=1.9e-07 Score=73.04 Aligned_cols=71 Identities=21% Similarity=0.289 Sum_probs=53.5
Q ss_pred cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCC-----------cccCCCCCceEEEEEcCH---HHHHHHHHHHHHH
Q 025165 151 GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP-----------LCASAHESDRVVQISGDV---PAVLNALVEIGNQ 216 (257)
Q Consensus 151 ~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p-----------~~~~~~~~~r~V~I~G~~---~~v~~A~~~I~~~ 216 (257)
.+++|.|||++|++||+|+++|||+|.|..+.... .... .+..-.|.|++.. +++.+|.++|..+
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~-~~eplhV~I~a~~~~~e~~~~A~~~I~~l 92 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAH-LNEPLHVLITAETPPEEALAKAVEAIEEL 92 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCccccc-CCCCcEEEEEeCCcHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999996431110 0000 0233679999964 8999999999999
Q ss_pred HhcCCC
Q 025165 217 LRENPP 222 (257)
Q Consensus 217 l~e~~~ 222 (257)
+.+..+
T Consensus 93 l~~~~~ 98 (120)
T cd02395 93 LKPAIE 98 (120)
T ss_pred hccCCC
Confidence 997543
No 31
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.51 E-value=1.7e-07 Score=77.88 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=54.4
Q ss_pred EEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEE---EcCHHHHHHHHHHHHHHHhc
Q 025165 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 147 l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I---~G~~~~v~~A~~~I~~~l~e 219 (257)
+.||.+.+|.|||++|++|+.|+++|||+|++.. .+..|.| +++++++.+|..+|..+.+.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~------------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 5689999999999999999999999999999942 2356888 89999999999999998885
No 32
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.49 E-value=4.7e-07 Score=72.76 Aligned_cols=103 Identities=17% Similarity=0.298 Sum_probs=72.7
Q ss_pred eEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCC
Q 025165 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~ 129 (257)
-.+.|+|+...+|+.||++|++|+.|++..|-+|++-... + +....|...+.......
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s---~-------------------d~~~fI~n~l~Pa~V~~ 89 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS---D-------------------DPEEFIKNIFAPAAVRS 89 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC---C-------------------CHHHHHHHHcCCCEEEE
Confidence 4688999999999999999999999999999888887531 1 11222333322110000
Q ss_pred chhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEE
Q 025165 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 130 ~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i 178 (257)
.. . ..........+.|+....|.+|||+|.+++.++.-+|-++.|
T Consensus 90 v~---I-~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 90 VT---I-KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EE---E-EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 00 0 000112356788999999999999999999999999998877
No 33
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.47 E-value=4e-07 Score=76.25 Aligned_cols=64 Identities=25% Similarity=0.260 Sum_probs=57.3
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE----cCHHHHHHHHHHHHHHHhc
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~----G~~~~v~~A~~~I~~~l~e 219 (257)
...+.||.+.+|.|||++|.+|+.|+++|||+|++.. .+..|.|. ++++++.+|.++|..++..
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~------------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS------------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC------------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 5688999999999999999999999999999999942 23678885 8999999999999999885
No 34
>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=98.46 E-value=4.5e-07 Score=70.94 Aligned_cols=72 Identities=19% Similarity=0.368 Sum_probs=51.7
Q ss_pred EEEecC------cccccccccCchhHHHHHhhhCceEEEcccccC-----------------CCccEEEecCCCCCchhh
Q 025165 53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIAR-----------------HEERVIIISSKDNDNVVS 109 (257)
Q Consensus 53 rilVP~------~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~-----------------~~ervv~I~G~~~~~~~~ 109 (257)
|+.||. +++|.|||++|.+||+|+++|||+|.|...-.. .+.--|.|++...+ ..
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~--~e 80 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPP--EE 80 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcH--HH
Confidence 455554 458999999999999999999999999954100 11245788887510 13
Q ss_pred HHHHHHHHHHHHHhcCC
Q 025165 110 DAENALQQIAALILKDD 126 (257)
Q Consensus 110 ~~~~a~~~I~~~i~~~~ 126 (257)
.+.+|+.+|..++....
T Consensus 81 ~~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 81 ALAKAVEAIEELLKPAI 97 (120)
T ss_pred HHHHHHHHHHHHhccCC
Confidence 67888888888886543
No 35
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.35 E-value=1.4e-06 Score=87.35 Aligned_cols=146 Identities=20% Similarity=0.285 Sum_probs=114.4
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCC
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~ 126 (257)
...+...+-+-...+..++||+|.+|.+|++++.+.+.+... +..+..+.++|... ...+|..++...+.+..
T Consensus 344 ~nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~-----~~~ka~~~v~~~~~ei~ 416 (753)
T KOG2208|consen 344 ENNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSA-----NDEKAVEDVEKIIAEIL 416 (753)
T ss_pred ccceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEecccc-----chhHHHHHHHHHHHhhh
Confidence 456888888999999999999999999999999999999985 46778888999854 46677777777776553
Q ss_pred CCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhC-CeEEEeCCCCCCcccCCCCCceEEEEEcCHHH
Q 025165 127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (257)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~ 205 (257)
.+ .....+.+|...+.++||.+|+.|..|..+++ .+|+.... .+....+++.|....
T Consensus 417 n~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~---------~~~~~~~~~~~~~~d 474 (753)
T KOG2208|consen 417 NS-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN---------NNSSDMVTIRGISKD 474 (753)
T ss_pred cc-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC---------CcccccceEeccccc
Confidence 32 12467899999999999999999999999999 66665322 134456788887777
Q ss_pred HHHHHHHHHHHHhcCC
Q 025165 206 VLNALVEIGNQLRENP 221 (257)
Q Consensus 206 v~~A~~~I~~~l~e~~ 221 (257)
+..+..+...+..+..
T Consensus 475 v~~~~~~~~~~~~~a~ 490 (753)
T KOG2208|consen 475 VEKSVSLLKALKADAK 490 (753)
T ss_pred cchhHHHHHhhhhhhh
Confidence 7777666666666533
No 36
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.33 E-value=1.1e-06 Score=82.95 Aligned_cols=162 Identities=20% Similarity=0.235 Sum_probs=114.1
Q ss_pred CCCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 45 ~~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
..+..+.+.+.+|...+++|+|++|++++.|+.-++++|.+.........+...|.+.... ...|..++.+.+.+
T Consensus 135 ~~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~-----~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 135 TENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKE-----VAAAKHLILEKVSE 209 (608)
T ss_pred hcCCcccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccch-----HHHHHhhhhccccc
Confidence 3466788899999999999999999999999999999999997744456777888886542 23344455554433
Q ss_pred CCCC------------------C------------------chh----hhh------------------------ccC--
Q 025165 125 DDDS------------------N------------------SEA----SKV------------------------AAG-- 138 (257)
Q Consensus 125 ~~~~------------------~------------------~~~----~~~------------------------~~~-- 138 (257)
.... + ... .+. .++
T Consensus 210 deelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~ 289 (608)
T KOG2279|consen 210 DEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSF 289 (608)
T ss_pred hhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCcccccc
Confidence 2110 0 000 000 000
Q ss_pred --CCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 025165 139 --HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN 215 (257)
Q Consensus 139 --~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 215 (257)
.....-..+.+|+..+|.+||+.|..++.+...+++.+.|... |.... -..-.++.+.|+..-+.+|..++..
T Consensus 290 ~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~---pyt~~-v~~~qic~~egkqh~~n~vl~ml~~ 364 (608)
T KOG2279|consen 290 QKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQ---PYTSR-VLQLQICVNEGKQHYENSVLEMLTV 364 (608)
T ss_pred ccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEec---cccch-hhhhhhheecchhHHHHHHHhhhhc
Confidence 0123346788999999999999999999999999999998642 22000 0122568899999999999998883
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=98.30 E-value=3.9e-06 Score=82.98 Aligned_cols=94 Identities=24% Similarity=0.307 Sum_probs=73.3
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025165 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (257)
Q Consensus 108 ~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (257)
+..+.+++..|++.+.+..... ... ....+....+.||.+.+|.|||+||.+||.|+++|||+|.|.
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~~~----s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-------- 614 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-DEM----SPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-------- 614 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-ccc----ccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence 4456778888888876543322 111 112345678999999999999999999999999999999983
Q ss_pred cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025165 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
.+..|.|.+ +.+++++|+.+|..++..
T Consensus 615 -----d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 615 -----DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -----cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 257788888 578999999999999995
No 38
>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=98.13 E-value=1.2e-05 Score=64.56 Aligned_cols=103 Identities=19% Similarity=0.281 Sum_probs=71.7
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~ 130 (257)
-+-|+|....+|+.||++|++|++|++..|-+|++-.. +++. ...|...+........
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey---s~D~-------------------~~fI~N~l~PA~V~~V 91 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY---SENL-------------------EEFVANKLAPAEVKNV 91 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc---CCCH-------------------HHHHHHcCCCceEEEE
Confidence 68899999999999999999999999999988888753 1110 1112221111000000
Q ss_pred hhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEe
Q 025165 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL 179 (257)
Q Consensus 131 ~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~ 179 (257)
.. ....+.....+.||.+..+..|||+|.+++...+-+|-++.|.
T Consensus 92 ---~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 92 ---TV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred ---EE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00 0011224678889999999999999999999999999988773
No 39
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.12 E-value=1.4e-05 Score=80.18 Aligned_cols=164 Identities=22% Similarity=0.270 Sum_probs=109.3
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCch--hhHHHHHHHHHHHHHh-cC
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNV--VSDAENALQQIAALIL-KD 125 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~--~~~~~~a~~~I~~~i~-~~ 125 (257)
-+..++.+-...++++||++|.+++.++.++.+.+.|++..-..+ ...+.|..+... ...++.++.++..-+. +.
T Consensus 200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~--~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~ 277 (753)
T KOG2208|consen 200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSP--SNKIDGRLNSSSSINVEIQEALTRLESEFDYDE 277 (753)
T ss_pred eEEEEeeccccchhhhccccccccccccccceeEEEcccccccch--hhhhccccccceehhhhhHHHHHHhcChhhhhh
Confidence 478999999999999999999999999999999999996532211 112222111100 0112233322211000 00
Q ss_pred ----------------------------CC------CCchhhhhc------------------cCCCcceEEEEEeccCc
Q 025165 126 ----------------------------DD------SNSEASKVA------------------AGHVAANTIRLLIAGSQ 153 (257)
Q Consensus 126 ----------------------------~~------~~~~~~~~~------------------~~~~~~~~~~l~Vp~~~ 153 (257)
.. ...+..+.. .-......+.+.+-...
T Consensus 278 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~ 357 (753)
T KOG2208|consen 278 IIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEE 357 (753)
T ss_pred hhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHh
Confidence 00 000000000 00012356778888999
Q ss_pred cceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 025165 154 AGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (257)
Q Consensus 154 vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~~~ 223 (257)
+..++|++|.+|.+|++.+.|.|.+... ++.+..+.++|...++.+|.+.+...+.+-+.+
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 9999999999999999999999998542 267889999999999999999999999997663
No 40
>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=98.01 E-value=1.9e-05 Score=78.78 Aligned_cols=93 Identities=23% Similarity=0.196 Sum_probs=67.5
Q ss_pred HHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccC
Q 025165 110 DAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCAS 189 (257)
Q Consensus 110 ~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 189 (257)
.+.+++..|++.+.+........ ..........+.||.+.+|.|||++|++||.|+++|||+|.|.
T Consensus 522 ~a~~~~~~I~~~m~~~l~~~~~~----~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~---------- 587 (684)
T TIGR03591 522 QAKEGRLHILGEMNKVISEPRAE----LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE---------- 587 (684)
T ss_pred HHHHHHHHHHHHHHHHHhhhhcc----ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe----------
Confidence 45666677777765432111000 0111234678999999999999999999999999999999984
Q ss_pred CCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025165 190 AHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 190 ~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
.+..|.|.+ +.+.+.+|..+|..+..+
T Consensus 588 ---ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 588 ---DDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred ---cCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 245677777 567899999999988775
No 41
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.77 E-value=8.9e-05 Score=62.43 Aligned_cols=103 Identities=20% Similarity=0.297 Sum_probs=70.9
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~ 130 (257)
.+-+.+-.+.+|..||++|.+|+.|+++.|-+|+|-... ++ -...|...+..-.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~d---------~~~fI~nal~Pa~---- 130 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------ED---------PAEFIKNALAPAE---- 130 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------CC---------HHHHHHHhcCcce----
Confidence 456666777899999999999999999999888877541 11 0112222222100
Q ss_pred hhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025165 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 131 ~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
...+.-...+.....+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus 131 -v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 131 -VLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred -EeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0000000001126788899999999999999999999999999999964
No 42
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.75 E-value=8.3e-05 Score=75.30 Aligned_cols=100 Identities=16% Similarity=0.196 Sum_probs=72.9
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCe-EEEeCCCCCCc
Q 025165 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL 186 (257)
Q Consensus 108 ~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~ 186 (257)
+..+.+++..|++.+.+........ ..........+.||.+.+|.|||+||.+||.|.++||++ |.+.
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------- 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKR----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence 4456677777777776543221110 111234567899999999999999999999999999999 8872
Q ss_pred ccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCCCCC
Q 025165 187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 187 ~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~~~~ 224 (257)
.+-.|.|.+ +.+.+++|+++|..++.+.....
T Consensus 723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~ 755 (891)
T PLN00207 723 ------DDGTVKITAKDLSSLEKSKAIISSLTMVPTVGD 755 (891)
T ss_pred ------CCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCc
Confidence 356788888 57899999999999987643333
No 43
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.74 E-value=4.7e-05 Score=75.44 Aligned_cols=66 Identities=33% Similarity=0.524 Sum_probs=56.0
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
.-...+.||.+.+|.|||+||.+||.|+++||++|+|.+ +..|.|.+... ..+++|+.+|..++..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~----~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADG----PSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCH----HHHHHHHHHHHHhhCc
Confidence 456788889999999999999999999999999999986 45688888653 3678888888888764
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.66 E-value=0.00019 Score=67.44 Aligned_cols=78 Identities=21% Similarity=0.259 Sum_probs=57.8
Q ss_pred ceEEEEEecc------CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCc---------ccCCCCCceEEEEEcC-HHH
Q 025165 142 ANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPL---------CASAHESDRVVQISGD-VPA 205 (257)
Q Consensus 142 ~~~~~l~Vp~------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~---------~~~~~~~~r~V~I~G~-~~~ 205 (257)
....+|.||- ++||.|||..|.+.|+|+++|||+|.|.-+..+-+ .......+=-+.|+++ .+.
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 3566888884 68999999999999999999999999974211100 0000123346888886 479
Q ss_pred HHHHHHHHHHHHhc
Q 025165 206 VLNALVEIGNQLRE 219 (257)
Q Consensus 206 v~~A~~~I~~~l~e 219 (257)
|++|++.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999996
No 45
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.64 E-value=0.00014 Score=70.92 Aligned_cols=100 Identities=22% Similarity=0.217 Sum_probs=75.9
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCc-hhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCc
Q 025165 108 VSDAENALQQIAALILKDDDSNS-EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPL 186 (257)
Q Consensus 108 ~~~~~~a~~~I~~~i~~~~~~~~-~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~ 186 (257)
...+..|..+|+..+.+-..... +.. ........+-|+.+.++-+||++|.+|++|.++|||+|++.
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~els-----~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------- 588 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKELS-----PYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhh-----ccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-------
Confidence 34567777888888765432211 111 11234678889999999999999999999999999999983
Q ss_pred ccCCCCCceEEEEEcCH-HHHHHHHHHHHHHHhcCCCCCc
Q 025165 187 CASAHESDRVVQISGDV-PAVLNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 187 ~~~~~~~~r~V~I~G~~-~~v~~A~~~I~~~l~e~~~~~~ 225 (257)
.+..|.|.++. +.+.+|++.|.++.++......
T Consensus 589 ------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~i 622 (692)
T COG1185 589 ------DDGTVKIAASDGESAKKAKERIEAITREVEVGEV 622 (692)
T ss_pred ------CCCcEEEEecchHHHHHHHHHHHHHHhhcccccE
Confidence 24668899876 7899999999999988666654
No 46
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.59 E-value=0.00015 Score=67.08 Aligned_cols=70 Identities=20% Similarity=0.231 Sum_probs=56.2
Q ss_pred CcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
.+.....+.|-+++||.|||++|++||+||..|+++|++..- ..+..|+|-|...--.+|...|...++.
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~----------~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC----------DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc----------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 345567888999999999999999999999999999999642 4678899999987666666555554443
No 47
>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=97.45 E-value=0.00016 Score=72.09 Aligned_cols=65 Identities=32% Similarity=0.456 Sum_probs=51.7
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHh
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~ 123 (257)
.-...+.||.+.++.|||+||.+||+|+++|||+|+|.+ +..|.|.+... ..+.+|.++|..+..
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~----~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDG----EAAEAAIKMIEGITA 614 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcH----HHHHHHHHHHHhhhc
Confidence 456788899999999999999999999999999999986 34566766542 256677777776654
No 48
>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=97.42 E-value=0.00021 Score=49.08 Aligned_cols=37 Identities=30% Similarity=0.504 Sum_probs=34.5
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEE
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i 85 (257)
+....+.|+.+.+|..|||+|.+|+.+++.++-+|+|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4678999999999999999999999999999988876
No 49
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.36 E-value=0.0035 Score=54.82 Aligned_cols=86 Identities=17% Similarity=0.252 Sum_probs=60.0
Q ss_pred CcceEEEEEecc------CccceeecCCChhHHHHHHHhCCeEEEeCCCCC------------Cccc-CCCCCceEEEEE
Q 025165 140 VAANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQL------------PLCA-SAHESDRVVQIS 200 (257)
Q Consensus 140 ~~~~~~~l~Vp~------~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~------------p~~~-~~~~~~r~V~I~ 200 (257)
....+.+|+||- ++||+|+|+.|.++|+|+++|||+|-|--+... |..+ ....---.|+..
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 345678899984 589999999999999999999999998632111 0000 000112467777
Q ss_pred cCHHHH----HHHHHHHHHHHhcCCCCCc
Q 025165 201 GDVPAV----LNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 201 G~~~~v----~~A~~~I~~~l~e~~~~~~ 225 (257)
+.+..+ ..|++.|.++|.-+.+...
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P~~e~~d 197 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVPDHEDED 197 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence 877654 4789999999888776644
No 50
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.32 E-value=0.00069 Score=62.50 Aligned_cols=97 Identities=21% Similarity=0.193 Sum_probs=65.9
Q ss_pred cccccccccCchhHHHHHhhh-CceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhcc
Q 025165 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (257)
Q Consensus 59 ~~vg~IIGkgG~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~ 137 (257)
+-+|+.||++|.+|+.|.++. |=+|+|-.. +++.. ..|...+.-.. ...+..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~---s~D~~-------------------~fI~Nal~Pa~-----V~~V~i 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEY---SNVPE-------------------IFIARALAPAI-----ISSVKI 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhCCCce-----eeEEEE
Confidence 348999999999999999997 888887754 11111 11111111000 000000
Q ss_pred CCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCC
Q 025165 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQ 183 (257)
Q Consensus 138 ~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~ 183 (257)
. .......+.||.++.+..|||+|.+++-..+-||.+|.|.+-.+
T Consensus 304 ~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 304 E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 0 11236789999999999999999999999999999999986443
No 51
>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=97.31 E-value=0.00072 Score=62.05 Aligned_cols=94 Identities=22% Similarity=0.333 Sum_probs=63.9
Q ss_pred ccccccccCchhHHHHHhhh-CceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025165 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138 (257)
Q Consensus 60 ~vg~IIGkgG~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~ 138 (257)
-+|+.||++|.+|+.|.++. |=+|+|-.. +++.. ..|...+.-.. ...+.-.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~---s~d~~-------------------~fi~nal~Pa~-----v~~v~i~ 296 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEY---SDDPA-------------------EFIANALSPAK-----VISVEVL 296 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhcCCce-----EEEEEEE
Confidence 38999999999999999998 888887754 11110 11111111000 0000000
Q ss_pred CCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025165 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
........+.||.++.+..|||+|.|++-..+-||.+|.|.+
T Consensus 297 ~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 297 DEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 001136899999999999999999999999999999999975
No 52
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.29 E-value=0.00051 Score=68.73 Aligned_cols=95 Identities=21% Similarity=0.202 Sum_probs=69.1
Q ss_pred hhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 025165 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (257)
Q Consensus 108 ~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~ 187 (257)
+..+.+++..|++.+.+......... .........+.||.+.++.+||+||.+||.|.++||+.|.+.
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-------- 590 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAEL----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhh----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--------
Confidence 33567777888888765432221111 111223457778999999999999999999999999998862
Q ss_pred cCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025165 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 188 ~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
.+..|.|.+ +.+.+.+|..+|..+..+
T Consensus 591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 -----DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 246688888 567999999999988875
No 53
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.25 E-value=0.00045 Score=64.91 Aligned_cols=72 Identities=24% Similarity=0.386 Sum_probs=54.2
Q ss_pred CeEEEEEecC------cccccccccCchhHHHHHhhhCceEEEccc------c---------cCC-CccEEEecCCCCCc
Q 025165 49 DVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA------I---------ARH-EERVIIISSKDNDN 106 (257)
Q Consensus 49 ~~~~rilVP~------~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~------~---------~~~-~ervv~I~G~~~~~ 106 (257)
.++-|+.||. ++||+|||..|.|.|+|+++|||||.|--. . ++. ++--|.|++...
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~-- 214 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ-- 214 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH--
Confidence 5677888885 469999999999999999999999999731 0 111 122377777654
Q ss_pred hhhHHHHHHHHHHHHHhc
Q 025165 107 VVSDAENALQQIAALILK 124 (257)
Q Consensus 107 ~~~~~~~a~~~I~~~i~~ 124 (257)
..+++|+..|..+|.+
T Consensus 215 --eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 215 --EKIKKAIAVIENLIQS 230 (554)
T ss_pred --HHHHHHHHHHHHHHHh
Confidence 3688888888888865
No 54
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.23 E-value=0.00037 Score=60.86 Aligned_cols=41 Identities=27% Similarity=0.614 Sum_probs=36.7
Q ss_pred CCCCeEEEEEecCc------ccccccccCchhHHHHHhhhCceEEEc
Q 025165 46 KAQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 46 ~~~~~~~rilVP~~------~vg~IIGkgG~~Ik~I~~~tga~I~i~ 86 (257)
+.-.++.||+||.. +||+|+|..|.++|+|+++|||+|-|-
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 34467889999976 699999999999999999999999997
No 55
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.23 E-value=0.00052 Score=61.65 Aligned_cols=71 Identities=24% Similarity=0.368 Sum_probs=57.6
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~ 221 (257)
....+.++.+..|.|||++|.+.++|+++|+++|.++.+.+ +.+-++.+.++.+.|.+|.+.|..+|.+.-
T Consensus 57 ~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~--------n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 57 FSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT--------NKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred chhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC--------CcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 45678899999999999999999999999999999875421 333444444477899999999999998854
No 56
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.21 E-value=0.00092 Score=61.79 Aligned_cols=95 Identities=24% Similarity=0.307 Sum_probs=64.8
Q ss_pred ccccccccCchhHHHHHhhh-CceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025165 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138 (257)
Q Consensus 60 ~vg~IIGkgG~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~ 138 (257)
-+|+.||++|.+|+.|.++. |=+|+|-... ++. ...|...+.... ...+.-.
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s---~d~-------------------~~fi~nal~Pa~-----v~~v~i~ 298 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWS---EDP-------------------AEFVANALSPAK-----VVSVEVD 298 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcC---CCH-------------------HHHHHHhCCCce-----EEEEEEE
Confidence 48999999999999999998 8888877541 111 011111111000 0000000
Q ss_pred CCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025165 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
........+.||.++.+..|||+|.|++-..+-||.+|.|.+.
T Consensus 299 ~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 299 DEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred cCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0112368999999999999999999999999999999999754
No 57
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.16 E-value=0.00043 Score=62.19 Aligned_cols=71 Identities=34% Similarity=0.377 Sum_probs=57.3
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
+....++|+++..|+|||++|.|.++|+++|+++|.++.+. ...-.+.|+|-. .+.|.+|..+|..+|.+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~--~n~~~i~i~~~~----~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN--TNKEEIKIIGIS----RNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC--CCcceEEEeehh----HHHHHHHHHHHHHHHHhh
Confidence 56778999999999999999999999999999999999873 233345565543 446788888888888654
No 58
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.15 E-value=0.0003 Score=62.66 Aligned_cols=65 Identities=18% Similarity=0.236 Sum_probs=57.8
Q ss_pred cceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 025165 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGN 215 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 215 (257)
+..+..+.||..+++.+.|++|.+||.|+.+|.++|.-+.+ ..+.++.++|..+.|..|+..|..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr----------~eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR----------GEEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC----------CCCCcceeccCchhHHHHhhcCcc
Confidence 45688899999999999999999999999999999998654 245789999999999999988865
No 59
>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=31% Similarity=0.451 Sum_probs=33.8
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEE
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i 178 (257)
....+.|+.+..|.+|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 478999999999999999999999999999999876
No 60
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.04 E-value=0.0017 Score=62.05 Aligned_cols=93 Identities=25% Similarity=0.349 Sum_probs=64.1
Q ss_pred cccccccCchhHHHHHhhh-CceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCC
Q 025165 61 IGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH 139 (257)
Q Consensus 61 vg~IIGkgG~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~ 139 (257)
+|+.||++|++|+.|.++. |=+|+|-.. +++.. ..|...+.... ...+...
T Consensus 247 vga~vG~~G~ri~~i~~el~ge~Idiv~~---s~d~~-------------------~fi~nal~pa~-----v~~v~~~- 298 (470)
T PRK09202 247 VGACVGMRGSRIQAISNELGGEKIDIILW---SDDPA-------------------QFIINALSPAE-----VSSVVVD- 298 (470)
T ss_pred hHccCCCCCchHHHHHHHhCCCeEEEEEc---CCCHH-------------------HHHHHhCCCCE-----EEEEEEe-
Confidence 8999999999999999998 888887754 11111 11111111000 0000000
Q ss_pred CcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025165 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
.....+.+.||..+.+..|||+|.|++-..+-||.+|.|...
T Consensus 299 ~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 299 EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 001368999999999999999999999999999999999863
No 61
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.02 E-value=0.0014 Score=61.63 Aligned_cols=94 Identities=23% Similarity=0.284 Sum_probs=63.4
Q ss_pred ccccccccCchhHHHHHhhh-CceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccC
Q 025165 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAG 138 (257)
Q Consensus 60 ~vg~IIGkgG~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~ 138 (257)
-+|+.||++|.+|+.|.++. |=+|+|-... ++.. ..|...+.-.. ...+...
T Consensus 278 PvGacVG~kG~RI~~I~~eL~gEkIDVI~ys---~Dp~-------------------~fI~NaLsPA~-----V~~V~i~ 330 (449)
T PRK12329 278 PVGACIGARGSRIQAVVNELRGEKIDVIRWS---PDPA-------------------TYIANALSPAR-----VDEVRLV 330 (449)
T ss_pred hhhccCCCCcchHHHHHHHhCCCeEEEEEcC---CCHH-------------------HHHHHhcCCce-----eeEEEEE
Confidence 48999999999999999998 8888877541 1111 11111111000 0000000
Q ss_pred CCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025165 139 HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 139 ~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
........+.||.++.+..|||+|.|++-..+-||.+|.|.+
T Consensus 331 ~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 331 DPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 001135789999999999999999999999999999999864
No 62
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.99 E-value=0.002 Score=56.17 Aligned_cols=68 Identities=21% Similarity=0.212 Sum_probs=56.8
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcC-HHHHHHHHHHHHHHHhcCCC
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLRENPP 222 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~-~~~v~~A~~~I~~~l~e~~~ 222 (257)
-+.+.||.+.++.+||++|.+|+.|.+.|++.|.+- .+..|.|.+. .+++.+|...|..+-+++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 366889999999999999999999999999999982 2466888886 45888898888888777665
Q ss_pred CC
Q 025165 223 RQ 224 (257)
Q Consensus 223 ~~ 224 (257)
++
T Consensus 213 ~~ 214 (235)
T PRK04163 213 SG 214 (235)
T ss_pred cC
Confidence 54
No 63
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.96 E-value=0.001 Score=61.84 Aligned_cols=55 Identities=25% Similarity=0.439 Sum_probs=48.2
Q ss_pred CCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCC
Q 025165 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~ 103 (257)
..+++.+.|.|-++.||.+||++|++|+.||..|+++|++... ..+-.|+|-|..
T Consensus 43 g~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 43 GGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred CCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 3568899999999999999999999999999999999999865 456678888864
No 64
>PRK00468 hypothetical protein; Provisional
Probab=96.85 E-value=0.0011 Score=47.56 Aligned_cols=34 Identities=35% Similarity=0.587 Sum_probs=30.0
Q ss_pred CCCCeEEEEEecCcccccccccCchhHHHHHhhh
Q 025165 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~t 79 (257)
..+.+.+++.|..+.+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456889999999999999999999999998764
No 65
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.85 E-value=0.0064 Score=58.89 Aligned_cols=65 Identities=22% Similarity=0.344 Sum_probs=54.5
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
+...+.+|+ ++-|+|||+.|.||+.+..-||+.|-|- ++...|+|+| +|-.-+.|...+..+|.+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid------------dtp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID------------DTPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc------------CCCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 355677888 5679999999999999999999999982 3456788999 888888888888888876
No 66
>PRK00106 hypothetical protein; Provisional
Probab=96.82 E-value=0.0077 Score=58.38 Aligned_cols=65 Identities=23% Similarity=0.387 Sum_probs=54.9
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
+...+.+|+ ++-|+|||+.|.||+.+..-||+.+.|- ++...|+|+| +|-.-+-|...+..++.+
T Consensus 225 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid------------dtp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 225 TITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID------------DTPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc------------CCCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 456677898 5779999999999999999999999982 3456788999 888888888888888876
No 67
>PRK12704 phosphodiesterase; Provisional
Probab=96.81 E-value=0.0071 Score=58.65 Aligned_cols=65 Identities=22% Similarity=0.336 Sum_probs=52.6
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhc
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e 219 (257)
+...+.+|+ ++-|+|||+.|.||+.+..-||+.|.|- ++...|.|+| +|-.-+.|...+..++.+
T Consensus 210 ~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid------------dtp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 210 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID------------DTPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred ceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc------------CCCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 355677888 5779999999999999999999999982 4456788999 677766777777777765
No 68
>PRK02821 hypothetical protein; Provisional
Probab=96.76 E-value=0.0013 Score=47.31 Aligned_cols=36 Identities=25% Similarity=0.434 Sum_probs=30.9
Q ss_pred CCCCeEEEEEecCcccccccccCchhHHHHHhhhCc
Q 025165 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (257)
Q Consensus 46 ~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga 81 (257)
..+...++|.|..+.+|.||||+|.+|+.||.--.+
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 345578999999999999999999999999987543
No 69
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.73 E-value=0.096 Score=44.57 Aligned_cols=134 Identities=14% Similarity=0.116 Sum_probs=87.0
Q ss_pred EEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchh
Q 025165 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132 (257)
Q Consensus 53 rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~ 132 (257)
.+.++....-.+...+|..++.|-...||+|.+... +..+.|+|++. .+..+...|.+.+..-
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~-----~~~~i~~~i~~~l~~i------- 91 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKS-----TAEYIEASINEILSNI------- 91 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHH-----HHHHHHHHHHHHHhhc-------
Confidence 344457788999999999999998889999999843 56799999864 2333333333333221
Q ss_pred hhhccCCCcceEEEEEeccCccceee----cCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEE-----cCH
Q 025165 133 SKVAAGHVAANTIRLLIAGSQAGCLI----GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDV 203 (257)
Q Consensus 133 ~~~~~~~~~~~~~~l~Vp~~~vG~iI----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~-----G~~ 203 (257)
.+..+-++.-.--..- -.....++.|++.|++.|.... ....+.|. -..
T Consensus 92 ----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~------------~~~~~~i~~~~~~~~~ 149 (210)
T PF14611_consen 92 ----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNP------------DGNKLKISWLASPENE 149 (210)
T ss_pred ----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECC------------CCCeEEEEEEeecccc
Confidence 1333333322111111 1235679999999999999742 22334444 456
Q ss_pred HHHHHHHHHHHHHHhcCCCCCc
Q 025165 204 PAVLNALVEIGNQLRENPPRQV 225 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~~~ 225 (257)
..+..|..++.-.+...++...
T Consensus 150 ~~~~~a~RlL~~a~~~~~~~~~ 171 (210)
T PF14611_consen 150 KRADRAKRLLLWALDYNPHSQE 171 (210)
T ss_pred chHHHHHHHHHHhccCCccccc
Confidence 7889999999999976666544
No 70
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.73 E-value=0.0016 Score=66.15 Aligned_cols=66 Identities=26% Similarity=0.420 Sum_probs=54.7
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCce-EEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT-IKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~-I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
.....+.||.+.++.|||.||.+||.|.++||++ |++.+ +-.|.|.+... ..+.+|..+|..+..+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~----~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDL----SSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCH----HHHHHHHHHHHHHhcC
Confidence 5677888999999999999999999999999999 88885 34577877653 3677888888887753
No 71
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.60 E-value=0.0047 Score=60.61 Aligned_cols=67 Identities=30% Similarity=0.413 Sum_probs=54.0
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
.-...+.|+.+.++.+||++|.+|++|.++||++|++.+. ..|.|.+...+ .+.+|+..|..+..+.
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~----~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGE----SAKKAKERIEAITREV 617 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchH----HHHHHHHHHHHHHhhc
Confidence 3456778899999999999999999999999999999843 34777776542 5778888888887543
No 72
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.60 E-value=0.0022 Score=45.91 Aligned_cols=32 Identities=41% Similarity=0.637 Sum_probs=29.2
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhh
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE 78 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~ 78 (257)
.....+++.+..+.+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45678999999999999999999999999876
No 73
>PRK12704 phosphodiesterase; Provisional
Probab=96.34 E-value=0.0091 Score=57.93 Aligned_cols=51 Identities=25% Similarity=0.484 Sum_probs=41.0
Q ss_pred CCeEEEEEecC-cccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCC
Q 025165 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (257)
Q Consensus 48 ~~~~~rilVP~-~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~ 103 (257)
..++-.+.+|+ +.-|+||||.|.|||.|+.-||+.|-|++. + .+|+|+|..
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~ 259 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD 259 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence 34555677788 558999999999999999999999999964 3 356688853
No 74
>PRK01064 hypothetical protein; Provisional
Probab=96.33 E-value=0.0036 Score=45.14 Aligned_cols=33 Identities=36% Similarity=0.708 Sum_probs=29.8
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhh
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~t 79 (257)
.+.+.+++.|..+..|.+|||+|.+|+.||.-.
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 466889999999999999999999999998863
No 75
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.18 E-value=0.01 Score=50.18 Aligned_cols=78 Identities=19% Similarity=0.243 Sum_probs=49.8
Q ss_pred ceEEEEEec------cCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCC-------CCCce--EEEEE-cCHHH
Q 025165 142 ANTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASA-------HESDR--VVQIS-GDVPA 205 (257)
Q Consensus 142 ~~~~~l~Vp------~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~-------~~~~r--~V~I~-G~~~~ 205 (257)
.++-++.|| .++||.|||+.|+++|+|++.|+|+|-|--.-..-+|-.. .+.+. -+.|. -+.+.
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedk 226 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDK 226 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhh
Confidence 345677777 4689999999999999999999999998532211111100 00111 12222 23456
Q ss_pred HHHHHHHHHHHHhc
Q 025165 206 VLNALVEIGNQLRE 219 (257)
Q Consensus 206 v~~A~~~I~~~l~e 219 (257)
++++++.+...|++
T Consensus 227 i~~~ik~~~n~I~~ 240 (269)
T COG5176 227 ICRLIKSQLNAIRE 240 (269)
T ss_pred HHHHHHHHHHHHHH
Confidence 67777777777777
No 76
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=96.08 E-value=0.013 Score=49.17 Aligned_cols=53 Identities=26% Similarity=0.319 Sum_probs=41.8
Q ss_pred ccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 60 QIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 60 ~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
..|+|||++|.|.+.|++-|+|+|.|... .|.|-|..+ .++.|...|..++..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------tVaiiG~~~-----~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------TVAIIGGFE-----QVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------EEEEecChh-----hhHHHHHHHHHHHcC
Confidence 36999999999999999999999999943 377778754 566666666666643
No 77
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=96.06 E-value=0.016 Score=48.85 Aligned_cols=157 Identities=17% Similarity=0.179 Sum_probs=98.5
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCc
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~ 130 (257)
+-++.||......+=--==...--|-+..+.+|.+. ...|.|.+.-.++....+..+++...|...+..++....
T Consensus 75 ~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmN-----lK~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DA 149 (252)
T KOG3273|consen 75 TRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMN-----LKARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDDA 149 (252)
T ss_pred eeeccCCcccCChHHHhhHhhhhHHHHhhhheeEee-----cccceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchhH
Confidence 456777777665442111111234556667777766 234556665544433356778888888887766544321
Q ss_pred hhh----hhc-cC--CCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCH
Q 025165 131 EAS----KVA-AG--HVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (257)
Q Consensus 131 ~~~----~~~-~~--~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~ 203 (257)
-.. ..+ .. -.+..+++=.=-+..+|+|+|++|.+--.|.+.|.++|.+. +..|.|-|..
T Consensus 150 iALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~~ 215 (252)
T KOG3273|consen 150 IALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGAF 215 (252)
T ss_pred HHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeecc
Confidence 000 000 00 00001111111245679999999999999999999999873 4669999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCcc
Q 025165 204 PAVLNALVEIGNQLRENPPRQVI 226 (257)
Q Consensus 204 ~~v~~A~~~I~~~l~e~~~~~~~ 226 (257)
+++..|...|+.+|...|...++
T Consensus 216 ~niriAR~avcsLIlGsppgkVy 238 (252)
T KOG3273|consen 216 QNIRIARDAVCSLILGSPPGKVY 238 (252)
T ss_pred hhhHHHHHhhHhhhccCCchhHH
Confidence 99999999999999998877643
No 78
>PRK02821 hypothetical protein; Provisional
Probab=96.02 E-value=0.0099 Score=42.77 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=26.8
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHh
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..+.+.+..+.+|+||||+|.+|+.||.--
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 578899999999999999999999998643
No 79
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.00 E-value=0.013 Score=56.68 Aligned_cols=50 Identities=26% Similarity=0.484 Sum_probs=40.7
Q ss_pred CCeEEEEEecC-cccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCC
Q 025165 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK 102 (257)
Q Consensus 48 ~~~~~rilVP~-~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~ 102 (257)
..++-.+.+|+ +.-|+||||.|.||+.|+..||+.|-|++. ++ .|+|++-
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----p~-~v~ls~f 252 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----PE-AVILSGF 252 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----CC-eEEecCC
Confidence 34566677888 558999999999999999999999999964 34 4668884
No 80
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.87 E-value=0.024 Score=54.64 Aligned_cols=98 Identities=19% Similarity=0.197 Sum_probs=71.9
Q ss_pred hHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCccc
Q 025165 109 SDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA 188 (257)
Q Consensus 109 ~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 188 (257)
..+..|...|++.+.+........ ..........+-|+.+....+||++|-..|+|..+||+.-++
T Consensus 567 ~~a~~ar~~Il~~m~k~i~~Pr~~----~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------- 632 (760)
T KOG1067|consen 567 QKAREARLQILDIMEKNINSPRGS----DKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------- 632 (760)
T ss_pred HhhhHHHHHHHHHHHhhcCCcccC----ccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee----------
Confidence 356677788888887654332111 112234567889999999999999999999999999954443
Q ss_pred CCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcCCCCC
Q 025165 189 SAHESDRVVQISG-DVPAVLNALVEIGNQLRENPPRQ 224 (257)
Q Consensus 189 ~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~~~~~ 224 (257)
++..+.|.- ++...++|.+.|..++....+.+
T Consensus 633 ----De~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~ 665 (760)
T KOG1067|consen 633 ----DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQD 665 (760)
T ss_pred ----cCceEEEEecCHHHHHHHHHHHHHHhcCccccc
Confidence 245677766 67899999999999998866654
No 81
>PRK00106 hypothetical protein; Provisional
Probab=95.86 E-value=0.016 Score=56.17 Aligned_cols=50 Identities=26% Similarity=0.530 Sum_probs=40.8
Q ss_pred CCeEEEEEecC-cccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCC
Q 025165 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSK 102 (257)
Q Consensus 48 ~~~~~rilVP~-~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~ 102 (257)
..++-.+.+|+ +.-|+||||.|.||+.|+.-||+.+-|++. ++ .|+|+|.
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----p~-~v~lS~f 273 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----PE-VVVLSGF 273 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----CC-eEEEeCC
Confidence 45566777898 558999999999999999999999999964 34 4558884
No 82
>PRK00468 hypothetical protein; Provisional
Probab=95.85 E-value=0.0096 Score=42.64 Aligned_cols=30 Identities=23% Similarity=0.390 Sum_probs=26.8
Q ss_pred ceEEEEEeccCccceeecCCChhHHHHHHH
Q 025165 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
...+++.+..+.+|+||||+|.+|+.||.-
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 367889999999999999999999999853
No 83
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.82 E-value=0.016 Score=50.62 Aligned_cols=60 Identities=28% Similarity=0.433 Sum_probs=46.8
Q ss_pred EEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHH
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAAL 121 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~ 121 (257)
+.+.||.+.++.+||++|.+|+.|.++|+++|.+-. +..|.|.+... ..+.+|.++|..+
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~----~~~~~a~~~I~~~ 206 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDE----EDEEIAIEAIKKI 206 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCH----HHHHHHHHHHHHH
Confidence 557889999999999999999999999999999864 35688888753 2345555555444
No 84
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.74 E-value=0.02 Score=48.49 Aligned_cols=42 Identities=21% Similarity=0.447 Sum_probs=35.7
Q ss_pred CCCeEEEEEecC------cccccccccCchhHHHHHhhhCceEEEccc
Q 025165 47 AQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 47 ~~~~~~rilVP~------~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
+..++-++.||. ++||+|||..|.|.|+|+..|+|+|-|--.
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 345677888884 569999999999999999999999999743
No 85
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.58 E-value=0.0093 Score=59.83 Aligned_cols=63 Identities=35% Similarity=0.527 Sum_probs=49.3
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHh
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~ 123 (257)
...+.||.+.++.+||+||.+||.|.++||++|++.+ +..|.|.+... ..+.+|.++|..+..
T Consensus 555 ~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~----~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 555 IETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDG----EAAEAAKERIEGITA 617 (693)
T ss_pred heeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccH----HHHHHHHHHHHHhcc
Confidence 4566669999999999999999999999999998864 34577777543 356777777777664
No 86
>PRK12705 hypothetical protein; Provisional
Probab=95.40 E-value=0.05 Score=52.52 Aligned_cols=66 Identities=21% Similarity=0.294 Sum_probs=48.0
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHHHHHHHHHhcC
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~~~I~~~l~e~ 220 (257)
+...+.+|+ ++-|+|||+.|.||+.+...||+.+.|- + +...|.|.+ +|..-+.|...+..+|.+.
T Consensus 198 tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d---------tp~~V~ls~fdp~rreia~~~l~~Li~dg 265 (508)
T PRK12705 198 SVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---D---------TPEAVVISSFNPIRREIARLTLEKLLADG 265 (508)
T ss_pred eeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---C---------CccchhhcccCccchHHHHHHHHHHHhcC
Confidence 345667887 4669999999999999999999999982 2 334466666 4555566666666666553
No 87
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.38 E-value=0.02 Score=41.05 Aligned_cols=30 Identities=33% Similarity=0.533 Sum_probs=26.9
Q ss_pred cceEEEEEeccCccceeecCCChhHHHHHH
Q 025165 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~ 170 (257)
....+++.+.....|.||||+|.+|+.||.
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHH
Confidence 345789999999999999999999999985
No 88
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=95.37 E-value=0.016 Score=46.59 Aligned_cols=38 Identities=26% Similarity=0.435 Sum_probs=34.1
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEc
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~ 86 (257)
...+.+.|+.+..|.+|||+|.|++.+++-++-+++|.
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 45677889999999999999999999999999888775
No 89
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.34 E-value=0.011 Score=41.80 Aligned_cols=36 Identities=17% Similarity=0.348 Sum_probs=30.4
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCce
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKAT 82 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~ 82 (257)
.+...+.+.+..+..|.+|||+|.+++.||.-.+.-
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~ 61 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAA 61 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHHH
Confidence 456678888899999999999999999999876543
No 90
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=95.32 E-value=0.028 Score=49.62 Aligned_cols=51 Identities=16% Similarity=0.249 Sum_probs=45.2
Q ss_pred ceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 155 G~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-++||++|+++|.|+--|.|.|-|. ...|.+.|....+..+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 4799999999999999999999983 35699999999999999888888776
No 91
>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=95.04 E-value=0.036 Score=37.68 Aligned_cols=35 Identities=29% Similarity=0.462 Sum_probs=29.1
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceE
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I 83 (257)
...+.+.+.....|.+|||+|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45666777776799999999999999999988554
No 92
>PRK01064 hypothetical protein; Provisional
Probab=95.00 E-value=0.03 Score=40.36 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=27.4
Q ss_pred cceEEEEEeccCccceeecCCChhHHHHHHH
Q 025165 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 141 ~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
....+++.+..+..|.+|||+|.+|+.||.-
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 3467889999999999999999999999864
No 93
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=94.97 E-value=0.022 Score=40.08 Aligned_cols=38 Identities=34% Similarity=0.552 Sum_probs=30.6
Q ss_pred EEEEEecCcc-----cccccccCchhHHHHHhhh-CceEEEccc
Q 025165 51 LFRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIADA 88 (257)
Q Consensus 51 ~~rilVP~~~-----vg~IIGkgG~~Ik~I~~~t-ga~I~i~~~ 88 (257)
..++.|-+.. +|..||++|..|+.|.++. |-+|+|-..
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 3577777777 9999999999999999999 888888754
No 94
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.17 E-value=0.023 Score=58.78 Aligned_cols=72 Identities=19% Similarity=0.144 Sum_probs=56.5
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc-ccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~-~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
....-++.+|-..++++||++|.+|+.++.-||+.|.+.+- ..+-.||.+.+.|.++ ..+-|-..|...+.+
T Consensus 1338 ~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~-----~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1338 PANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPP-----SQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCCh-----hhhhhhccccceeec
Confidence 34567889999999999999999999999999999999974 3346799999999975 344444445444443
No 95
>PRK12705 hypothetical protein; Provisional
Probab=93.75 E-value=0.1 Score=50.43 Aligned_cols=40 Identities=28% Similarity=0.442 Sum_probs=34.1
Q ss_pred CeEEEEEecCc-ccccccccCchhHHHHHhhhCceEEEccc
Q 025165 49 DVLFRIIVPSR-QIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 49 ~~~~rilVP~~-~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
.++-.+.+|++ .-|+||||.|.||+.++..||+.|-|++.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 44556667774 48999999999999999999999999964
No 96
>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=93.25 E-value=0.056 Score=38.54 Aligned_cols=35 Identities=40% Similarity=0.608 Sum_probs=29.8
Q ss_pred eEEEEEecCcccccccccCchhHHHHHhhhCceEE
Q 025165 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK 84 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~ 84 (257)
..+.+.+.....|.+||++|++|++|++...-.+.
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 45788899999999999999999999888765553
No 97
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=93.10 E-value=0.092 Score=36.92 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=30.7
Q ss_pred EEEEEeccCc-----cceeecCCChhHHHHHHHh-CCeEEEeC
Q 025165 144 TIRLLIAGSQ-----AGCLIGMSGQNIEKLRNSS-GATIVILA 180 (257)
Q Consensus 144 ~~~l~Vp~~~-----vG~iIGk~G~~Ik~I~~~t-ga~I~i~~ 180 (257)
...+.|-... +|..||++|++|+.|.++. |-+|.+..
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 4567777777 8999999999999999999 99999874
No 98
>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=93.04 E-value=0.082 Score=42.50 Aligned_cols=39 Identities=28% Similarity=0.371 Sum_probs=34.8
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~ 86 (257)
+.....+.||.+..++.|||+|.|++...+-++-+++|.
T Consensus 98 ~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 98 GKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 456678889999999999999999999999999888775
No 99
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=93.01 E-value=0.13 Score=42.39 Aligned_cols=47 Identities=19% Similarity=0.294 Sum_probs=37.8
Q ss_pred ccccCCCCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc
Q 025165 41 PKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 41 ~~~~~~~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
.+.++...+-.+-|+|-... |..|||+|.+|+++++..|-+|.+-+.
T Consensus 52 ~~~k~~~~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 52 EYKKAYEVDDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred eEEEEEEeCCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 34444444556778887778 999999999999999999999998864
No 100
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=92.99 E-value=0.046 Score=56.67 Aligned_cols=71 Identities=23% Similarity=0.205 Sum_probs=59.3
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
.+-++-+|-....+|||++|++|..++..||+.|++.+-. +. ...+|.+.+.|.++.+..|...|.-.+-+
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 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--PD----NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--Cc----cchhhhcccCCCChhhhhhhccccceeec
Confidence 3456788888899999999999999999999999996411 22 25789999999999999998888776665
No 101
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.82 E-value=0.069 Score=37.65 Aligned_cols=32 Identities=38% Similarity=0.547 Sum_probs=27.5
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCC
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGA 174 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga 174 (257)
..+.+.+..+..|.||||.|.+++.||--.+.
T Consensus 29 ~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 29 DTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 46888899999999999999999999865543
No 102
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=92.69 E-value=0.24 Score=43.09 Aligned_cols=66 Identities=20% Similarity=0.246 Sum_probs=50.9
Q ss_pred EEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHH-HHHHHHHHHHHHHhcCCCC
Q 025165 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVP-AVLNALVEIGNQLRENPPR 223 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~-~v~~A~~~I~~~l~e~~~~ 223 (257)
.-+.|+...|.++||++|+.++-|.+.|+|.|.+- ....|-|.|..+ ....|...|..+=+|+...
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG-------------~NG~IWV~~~~~~~e~~~~~aI~~ie~ea~~~ 214 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG-------------QNGRIWVDGENESLEELAIEAIRKIEREAHTS 214 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe-------------cCCEEEecCCCcchHHHHHHHHHHHhhhhhhh
Confidence 55789999999999999999999999999999984 235577777766 4556666666665555443
No 103
>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=92.52 E-value=0.23 Score=33.59 Aligned_cols=34 Identities=32% Similarity=0.459 Sum_probs=26.9
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeE
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI 176 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I 176 (257)
....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 3455666665689999999999999999887544
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=92.41 E-value=0.12 Score=36.84 Aligned_cols=35 Identities=17% Similarity=0.373 Sum_probs=28.5
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEE
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i 85 (257)
.+.+.+..+..|.+|||+|+++..||--.+.-++-
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 45666778889999999999999999887755543
No 105
>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=91.76 E-value=0.11 Score=36.92 Aligned_cols=35 Identities=34% Similarity=0.564 Sum_probs=29.5
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEE
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV 177 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~ 177 (257)
....+.+..++-|.+||++|++|++|.+..+-.+.
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 35788899999999999999999999877665553
No 106
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=91.72 E-value=0.17 Score=42.72 Aligned_cols=37 Identities=27% Similarity=0.416 Sum_probs=35.2
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEcc
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~ 87 (257)
...+.||.+..+..|||+|.+++.+.+-||-+++|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7888999999999999999999999999999999984
No 107
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=91.29 E-value=0.15 Score=48.38 Aligned_cols=40 Identities=35% Similarity=0.482 Sum_probs=35.6
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
+-...+.||...++.+|||+|.+|++|++..|.+|+|-..
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 4456778899999999999999999999999999999843
No 108
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=90.99 E-value=0.27 Score=45.65 Aligned_cols=41 Identities=24% Similarity=0.244 Sum_probs=37.2
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
+.....+.||.+..+..|||+|.|++-..+-||.+|+|-..
T Consensus 306 ~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 306 EEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred CCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 44578899999999999999999999999999999999843
No 109
>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=90.74 E-value=0.29 Score=45.02 Aligned_cols=40 Identities=23% Similarity=0.361 Sum_probs=36.7
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~ 87 (257)
+.....+.||.+..+..|||+|.|++...+-||.+|+|-.
T Consensus 299 ~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 299 DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 3467899999999999999999999999999999999974
No 110
>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=90.46 E-value=2 Score=34.59 Aligned_cols=95 Identities=14% Similarity=0.300 Sum_probs=64.3
Q ss_pred ccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcce
Q 025165 64 VIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAAN 143 (257)
Q Consensus 64 IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~~ 143 (257)
.+=.+|..|++|-++..-+|.|-... . +.- +-.+|...|.+++-++..-..-.. +..
T Consensus 20 ~~~~~~dli~~lAk~lrKRIvvR~dp-----s---~l~--------~~e~A~~~I~~ivP~ea~i~di~F-------d~~ 76 (145)
T cd02410 20 LFAEDGDLVKDLAKDLRKRIVIRPDP-----S---VLK--------PPEEAIKIILEIVPEEAGITDIYF-------DDD 76 (145)
T ss_pred HHhcccHHHHHHHHHHhceEEEcCCh-----h---hcC--------CHHHHHHHHHHhCCCccCceeeEe-------cCC
Confidence 44456788899988888777775221 0 111 224678888888754422110000 012
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
+-++.|-...-|.+||++|.++++|..+||-.-.+...
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 45778888888999999999999999999999998754
No 111
>PRK13764 ATPase; Provisional
Probab=90.40 E-value=0.23 Score=49.11 Aligned_cols=41 Identities=37% Similarity=0.528 Sum_probs=36.6
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
.+....+.||...++.+|||+|.+|++|++..|.+|+|-..
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 45566788999999999999999999999999999999743
No 112
>PRK13764 ATPase; Provisional
Probab=89.68 E-value=0.57 Score=46.36 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=38.6
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCC
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP 185 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p 185 (257)
....+.||...++.+|||+|.+|++|.++.|.+|.|.+.++.+
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4678999999999999999999999999999999998765543
No 113
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=89.31 E-value=0.37 Score=34.90 Aligned_cols=37 Identities=19% Similarity=0.412 Sum_probs=30.7
Q ss_pred eEEEEEecCcccccccccCchhHHHHHhhhCceEEEc
Q 025165 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~ 86 (257)
..+++.|....-|.|||++|++|++|+++-.-...+.
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3478888999999999999999999999876555553
No 114
>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=89.16 E-value=0.45 Score=33.93 Aligned_cols=34 Identities=26% Similarity=0.509 Sum_probs=27.3
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEE
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV 177 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~ 177 (257)
...+.+.....|.+|||.|.+++.||--+..-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 4677778888999999999999999866554443
No 115
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=88.87 E-value=0.5 Score=43.88 Aligned_cols=42 Identities=29% Similarity=0.402 Sum_probs=37.7
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
++.....+.||.+..+..|||+|.|++.-.+-||.+|+|-..
T Consensus 300 ~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 300 EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 344678999999999999999999999999999999999854
No 116
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=88.68 E-value=2.8 Score=35.51 Aligned_cols=66 Identities=18% Similarity=0.234 Sum_probs=55.2
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~ 221 (257)
...+.++....-.+...+|..+++|....||+|.+. .....+.|+|+...+..+...|.++++..-
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~------------~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVS------------RSENRIRITGTKSTAEYIEASINEILSNIR 92 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEe------------cCCcEEEEEccHHHHHHHHHHHHHHHhhcE
Confidence 345556677888899999999999988899999985 345789999999999999999988887743
No 117
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=88.63 E-value=0.41 Score=45.97 Aligned_cols=39 Identities=26% Similarity=0.392 Sum_probs=36.3
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcc
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~ 87 (257)
...+.+.||.+..+..|||+|.|++...+-||.+|+|..
T Consensus 301 ~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 301 EHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 357899999999999999999999999999999999975
No 118
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.58 E-value=0.29 Score=41.36 Aligned_cols=56 Identities=32% Similarity=0.440 Sum_probs=46.4
Q ss_pred CcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 58 SRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 58 ~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
+..+|+|+||+|.+--.|++.|..+|.+.+. .+.|-|. +.+++-|...|+.+|...
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~-------kIHiLG~-----~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS-------KIHILGA-----FQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc-------eEEEeec-----chhhHHHHHhhHhhhccC
Confidence 4578999999999999999999999999854 3667776 446888888899988754
No 119
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.46 E-value=0.38 Score=45.81 Aligned_cols=40 Identities=15% Similarity=0.235 Sum_probs=36.5
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (257)
....+.||...++.+|||+|.+|++|.++.|.+|.|...+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 4678899999999999999999999999999999997654
No 120
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=87.15 E-value=0.59 Score=44.32 Aligned_cols=41 Identities=29% Similarity=0.433 Sum_probs=37.0
Q ss_pred CCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEccc
Q 025165 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (257)
Q Consensus 48 ~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~ 88 (257)
+.....+.||.+..+..|||+|.|++--.+-||.+|+|...
T Consensus 333 ~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 333 EGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred CCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 34567899999999999999999999999999999999853
No 121
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.93 E-value=2.3 Score=41.08 Aligned_cols=97 Identities=16% Similarity=0.298 Sum_probs=68.7
Q ss_pred ccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCc
Q 025165 62 GKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVA 141 (257)
Q Consensus 62 g~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~ 141 (257)
-.++=+.|.-||+|-++..-+|.|-... + + +.+-.+|.+.|.+++-++..-..-.. +
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~dP--s------v--------l~~~e~A~~~I~eivP~ea~i~~i~F-------d 97 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPDP--S------V--------LKPPEEARKIILEIVPEEAGITDIYF-------D 97 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccCc--h------h--------cCCHHHHHHHHHHhCccccCceeEEe-------c
Confidence 4566788999999999998888876321 0 0 11235788888888854432111000 1
Q ss_pred ceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCC
Q 025165 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (257)
Q Consensus 142 ~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~ 181 (257)
..+-+++|-...-|.+|||+|++.++|..+||-.-.|.+.
T Consensus 98 ~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 98 DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 1245788888899999999999999999999998888764
No 122
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=86.69 E-value=0.98 Score=37.28 Aligned_cols=36 Identities=19% Similarity=0.340 Sum_probs=31.3
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeC
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~ 180 (257)
..-++|-... |..||++|.+++.+++..|-+|.+..
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 4667776666 99999999999999999999999874
No 123
>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=86.38 E-value=1 Score=32.56 Aligned_cols=36 Identities=14% Similarity=0.312 Sum_probs=29.2
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEE
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i 178 (257)
...++.|....-|.|||++|+.|++|++.-.-...+
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 357888888999999999999999998776544443
No 124
>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=86.31 E-value=0.69 Score=35.38 Aligned_cols=31 Identities=29% Similarity=0.549 Sum_probs=26.2
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCc
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga 81 (257)
.+++.|-...-|.|||++|++|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 3677888888999999999999999887543
No 125
>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=85.34 E-value=0.85 Score=33.18 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=23.4
Q ss_pred EEEEecCcccccccccCchhHHHHHhhh
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~t 79 (257)
+++.|....-|.+||++|++|++|++.-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5566666889999999999999998774
No 126
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=84.74 E-value=1.1 Score=36.01 Aligned_cols=38 Identities=29% Similarity=0.449 Sum_probs=32.5
Q ss_pred EEEecCcccccccccCchhHHHHHhhhCceEEEccccc
Q 025165 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90 (257)
Q Consensus 53 rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 90 (257)
.+.|-...-|.+|||+|.+++.|..+||-+-.+.+..|
T Consensus 79 EV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 79 EVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred EEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 56667788999999999999999999998888876543
No 127
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=84.68 E-value=1.6 Score=42.56 Aligned_cols=67 Identities=25% Similarity=0.252 Sum_probs=49.4
Q ss_pred CCCeEEEEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhc
Q 025165 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (257)
Q Consensus 47 ~~~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~ 124 (257)
.......+.|+.+....+||.+|...|+|+.+||+.-.++ |..+.|-.... ....+|...|..++..
T Consensus 594 y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~----~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 594 YSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQ----AAMEEAKEFIDGIIKD 660 (760)
T ss_pred cCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCH----HHHHHHHHHHHHHhcC
Confidence 3567788999999999999999999999999999554444 33466656532 2446666666666654
No 128
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=82.79 E-value=1.1 Score=38.92 Aligned_cols=46 Identities=22% Similarity=0.480 Sum_probs=38.6
Q ss_pred EEEecCcccccccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCC
Q 025165 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN 104 (257)
Q Consensus 53 rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~ 104 (257)
-+.|++..|-++||++|+.++.|.++++|+|-+-.. ..+-|.+..+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~ 194 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE 194 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence 467899999999999999999999999999998742 3466777665
No 129
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=82.00 E-value=1.6 Score=41.95 Aligned_cols=125 Identities=12% Similarity=0.078 Sum_probs=76.2
Q ss_pred cccccCchhHHHHHhhhCceEEEc--ccccCCCccEEE-ecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCC
Q 025165 63 KVIGKEGHRIQKIREETKATIKIA--DAIARHEERVII-ISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGH 139 (257)
Q Consensus 63 ~IIGkgG~~Ik~I~~~tga~I~i~--~~~~~~~ervv~-I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~ 139 (257)
.|-||+--.+.+|++...|.+.+. +. .+.++.+ +.|..- +-++++. .+..+ .
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~---~gs~~~~~~~g~~~-----~F~k~~~----~~~~E----F--------- 447 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS---TGSIVETNGIGEKM-----SFSKKLS----IPPTE----F--------- 447 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec---CCcEEEEeccCcch-----hhHHHhc----CCccc----C---------
Confidence 677886666999999999985544 33 2234443 344321 2222221 11110 0
Q ss_pred CcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceE-EEEEcC---HHHHHHHHHHHHH
Q 025165 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV-VQISGD---VPAVLNALVEIGN 215 (257)
Q Consensus 140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~-V~I~G~---~~~v~~A~~~I~~ 215 (257)
.....+.||...|..|||.||..|.+++.+.++.|++...-.++. +.-+- |.|.-. .+++.-+.--+++
T Consensus 448 --pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q-----s~~~dNV~I~~PrKn~~ni~~~KNd~~~ 520 (657)
T COG5166 448 --PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ-----SQWHDNVLIEAPRKNQDNISGKKNDKLD 520 (657)
T ss_pred --chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch-----hhhhcceEEECCccCccchhcccccHHH
Confidence 024789999999999999999999999999999999754333333 22222 444442 2345555555666
Q ss_pred HHhc
Q 025165 216 QLRE 219 (257)
Q Consensus 216 ~l~e 219 (257)
++++
T Consensus 521 ~V~~ 524 (657)
T COG5166 521 KVKQ 524 (657)
T ss_pred HHhh
Confidence 6664
No 130
>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=80.72 E-value=2 Score=31.21 Aligned_cols=29 Identities=28% Similarity=0.469 Sum_probs=23.6
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHh
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..++.|....-|.+||++|++|++|++.-
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 36667777888999999999999987543
No 131
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=80.69 E-value=1.3 Score=38.33 Aligned_cols=31 Identities=35% Similarity=0.529 Sum_probs=27.0
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhh
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~t 79 (257)
...+++.|....-|.||||+|++|++|++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 5567888899999999999999999987764
No 132
>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=80.49 E-value=1.8 Score=33.10 Aligned_cols=29 Identities=34% Similarity=0.594 Sum_probs=24.7
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHh
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
.+++.|....-|.|||++|+.|++|++..
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l 90 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKEL 90 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHH
Confidence 46788888888999999999999998654
No 133
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=79.42 E-value=2.3 Score=40.92 Aligned_cols=127 Identities=13% Similarity=0.150 Sum_probs=80.0
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCceEEEccc--ccCCCcc-EEEecCCCCCchhhHHHHHHHHHHHHHhcCCC
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA--IARHEER-VIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~--~~~~~er-vv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~ 127 (257)
.+.+.||...|..|||-||..|++++.+.++.|++... .+.+--+ .|.|..+..+.. .+.-+...+.+++.+.+.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~--ni~~~KNd~~~~V~~~c~ 527 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQD--NISGKKNDKLDKVKQQCR 527 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCcc--chhcccccHHHHHhhhcc
Confidence 47789999999999999999999999999999998843 1122222 266766555422 233333444555544332
Q ss_pred CCchh---------------------hhhccC----CCcceEEEEEeccCccceeec---CCChhHHHHHHHhCCeEEEe
Q 025165 128 SNSEA---------------------SKVAAG----HVAANTIRLLIAGSQAGCLIG---MSGQNIEKLRNSSGATIVIL 179 (257)
Q Consensus 128 ~~~~~---------------------~~~~~~----~~~~~~~~l~Vp~~~vG~iIG---k~G~~Ik~I~~~tga~I~i~ 179 (257)
.+... ..+... .......-+.+|+..++..+| -.|++|..+.....-.|...
T Consensus 528 f~~Kgdirf~~~~~sI~~v~~~~~~I~rv~kne~v~~~~p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~~ 607 (657)
T COG5166 528 FNLKGDIRFCPQSTSIFTVDIYSDEIERVIKNETVLLEFPAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEFS 607 (657)
T ss_pred cccccceEEcCCceEEEEEcccccHHHHHhhccceEEecccccccccchhhhhccCCcccccccchhhhhhhhhccceee
Confidence 11000 000000 011234556788888999999 67888888888777777764
No 134
>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=79.08 E-value=5.9 Score=39.58 Aligned_cols=97 Identities=14% Similarity=0.274 Sum_probs=66.1
Q ss_pred cccccCchhHHHHHhhhCceEEEcccccCCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcCCCCCchhhhhccCCCcc
Q 025165 63 KVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAA 142 (257)
Q Consensus 63 ~IIGkgG~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~~~~~~~~~~~~~~~~~~ 142 (257)
..+=.+|..|++|-++..-+|.|-... . +.-+ -.+|.+.|.+++-++..-..-.. +.
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~~-----~---~~~~--------~~~~~~~i~~~~~~~~~~~~~~f-------~~ 92 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPDP-----S---VLLP--------PEEAIEKIKEIVPEEAGITDIYF-------DD 92 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecCh-----h---hcCC--------HHHHHHHHHHhCCCcCCceeEEe-------cC
Confidence 445567888899988888777775221 0 1111 24677888887754422110000 11
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCC
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~ 182 (257)
.+-+++|-...-|.||||+|+++++|.++||-.-.|.+..
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 2457888888899999999999999999999999987643
No 135
>PF08067 ROKNT: ROKNT (NUC014) domain; InterPro: IPR012987 This presumed domain is found at the N terminus of RNP K-like proteins that also contain KH domains IPR004088 from INTERPRO [].
Probab=79.06 E-value=0.78 Score=28.48 Aligned_cols=30 Identities=20% Similarity=0.170 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCCCCCCccCCCCCCCCCCccccCCC
Q 025165 13 VSVVTEPEPRHDVSGKRRREDGEIEGSDPKRRAKA 47 (257)
Q Consensus 13 ~~~~~~~~~~~~~~~kr~~e~~~~~~~~~~~~~~~ 47 (257)
+..+|++.+.|+ ||+.||+++ .+++|+++.
T Consensus 9 ~e~tF~n~etNG---KrpaeDmeE--e~afKRsrN 38 (43)
T PF08067_consen 9 EEETFSNTETNG---KRPAEDMEE--EQAFKRSRN 38 (43)
T ss_pred ccccccccccCC---CCchhhHHH--HHHhccccc
Confidence 567799999998 999999884 456666554
No 136
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=77.10 E-value=5.2 Score=35.71 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=24.3
Q ss_pred cccccccCchhHHHHHhhhCceEEEc
Q 025165 61 IGKVIGKEGHRIQKIREETKATIKIA 86 (257)
Q Consensus 61 vg~IIGkgG~~Ik~I~~~tga~I~i~ 86 (257)
--++||.+|+|+|.|+=-|.|.|-|.
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVq 185 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQ 185 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEee
Confidence 35799999999999999999999998
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=77.07 E-value=4.6 Score=35.08 Aligned_cols=32 Identities=41% Similarity=0.618 Sum_probs=26.7
Q ss_pred eEEEEEeccCccceeecCCChhHHHHH----HHhCC
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLR----NSSGA 174 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~----~~tga 174 (257)
...++.|....=|.|||++|++|++|+ +.+|.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 467888888999999999999999886 45555
No 138
>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=72.27 E-value=4.8 Score=35.40 Aligned_cols=29 Identities=21% Similarity=0.248 Sum_probs=22.3
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHHHH
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~~~ 171 (257)
+...++|.. ++-+.|||++|+.||+|...
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 456677775 45699999999999988644
No 139
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=68.37 E-value=5.4 Score=35.06 Aligned_cols=30 Identities=27% Similarity=0.284 Sum_probs=23.4
Q ss_pred eEEEEEecCcc-cccccccCchhHHHHHhhh
Q 025165 50 VLFRIIVPSRQ-IGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 50 ~~~rilVP~~~-vg~IIGkgG~~Ik~I~~~t 79 (257)
+...|+|..+. .+-||||+|+.||+|..+.
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 66777887655 6778899999999986553
No 140
>PRK15494 era GTPase Era; Provisional
Probab=67.27 E-value=6.9 Score=35.85 Aligned_cols=36 Identities=14% Similarity=0.279 Sum_probs=26.2
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHH--------HHhCCeEEE
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLR--------NSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~--------~~tga~I~i 178 (257)
+...++|.. ++-+.|||++|+.||+|. +-+|++|.+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 445667775 466999999999999885 445666654
No 141
>COG1159 Era GTPase [General function prediction only]
Probab=65.46 E-value=8.2 Score=34.83 Aligned_cols=35 Identities=26% Similarity=0.472 Sum_probs=25.5
Q ss_pred EEEEEecc-CccceeecCCChhHHHHH--------HHhCCeEEE
Q 025165 144 TIRLLIAG-SQAGCLIGMSGQNIEKLR--------NSSGATIVI 178 (257)
Q Consensus 144 ~~~l~Vp~-~~vG~iIGk~G~~Ik~I~--------~~tga~I~i 178 (257)
...++|+. ++-|.|||++|++||+|- +-.+++|.+
T Consensus 230 ~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 230 HATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 44566775 566999999999999874 445666554
No 142
>PRK00089 era GTPase Era; Reviewed
Probab=65.20 E-value=8 Score=34.22 Aligned_cols=36 Identities=22% Similarity=0.422 Sum_probs=25.9
Q ss_pred eEEEEEecc-CccceeecCCChhHHHHH--------HHhCCeEEE
Q 025165 143 NTIRLLIAG-SQAGCLIGMSGQNIEKLR--------NSSGATIVI 178 (257)
Q Consensus 143 ~~~~l~Vp~-~~vG~iIGk~G~~Ik~I~--------~~tga~I~i 178 (257)
+...+.|.. ++-+.|||++|++||+|. +-+|++|.+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 345566664 466999999999999875 455666654
No 143
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=64.55 E-value=3.9 Score=34.90 Aligned_cols=37 Identities=14% Similarity=0.299 Sum_probs=30.2
Q ss_pred CeEEEEEecCcccccccccCchhHHHHHhhhCceEEE
Q 025165 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (257)
Q Consensus 49 ~~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i 85 (257)
.-.+.+.+-.+..+.+||+.|.++..||--+++.++-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3445566677779999999999999999998877665
No 144
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=63.85 E-value=6.4 Score=33.65 Aligned_cols=30 Identities=30% Similarity=0.496 Sum_probs=24.4
Q ss_pred EEEEecCcccccccccCchhHHHHHhhhCc
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~tga 81 (257)
+++.|....-|.+||++|++|++|++.-.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 555556688999999999999999887644
No 145
>PRK15494 era GTPase Era; Provisional
Probab=61.83 E-value=8.3 Score=35.31 Aligned_cols=29 Identities=24% Similarity=0.439 Sum_probs=22.7
Q ss_pred eEEEEEecCcc-cccccccCchhHHHHHhh
Q 025165 50 VLFRIIVPSRQ-IGKVIGKEGHRIQKIREE 78 (257)
Q Consensus 50 ~~~rilVP~~~-vg~IIGkgG~~Ik~I~~~ 78 (257)
+...|+|..+. -+.||||+|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 55677887665 677889999999998554
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=61.70 E-value=5.8 Score=38.39 Aligned_cols=38 Identities=32% Similarity=0.474 Sum_probs=33.0
Q ss_pred EEEecCcccccccccCchhHHHHHhhhCceEEEccccc
Q 025165 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90 (257)
Q Consensus 53 rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 90 (257)
.++|-...-|.+|||+|++.+.|.++||-.-.|.+..|
T Consensus 102 EViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP 139 (637)
T COG1782 102 EVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP 139 (637)
T ss_pred eEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC
Confidence 56677888999999999999999999998888876544
No 147
>CHL00048 rps3 ribosomal protein S3
Probab=61.30 E-value=7.5 Score=33.41 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=26.0
Q ss_pred eEEEEEecCcccccccccCchhHHHHHhhhC
Q 025165 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tg 80 (257)
..+++.|-...-|.|||++|.+|++|++...
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 3467777788889999999999999988763
No 148
>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=60.80 E-value=8 Score=32.77 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=26.2
Q ss_pred eEEEEEecCcccccccccCchhHHHHHhhhC
Q 025165 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 50 ~~~rilVP~~~vg~IIGkgG~~Ik~I~~~tg 80 (257)
..+++.|....-|.+||++|..|++|+++-.
T Consensus 38 ~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 38 LGTKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred CcEEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 3477888888899999999999999987754
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=60.06 E-value=9.2 Score=33.83 Aligned_cols=30 Identities=33% Similarity=0.455 Sum_probs=22.1
Q ss_pred eEEEEEecCcc-cccccccCchhHHHHHhhh
Q 025165 50 VLFRIIVPSRQ-IGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 50 ~~~rilVP~~~-vg~IIGkgG~~Ik~I~~~t 79 (257)
+...|.|..+. .+.||||+|+.||+|....
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 55566666544 6788899999999986553
No 150
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=59.82 E-value=24 Score=32.59 Aligned_cols=57 Identities=26% Similarity=0.252 Sum_probs=45.6
Q ss_pred eccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHH--HHHhc
Q 025165 149 IAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG--NQLRE 219 (257)
Q Consensus 149 Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~--~~l~e 219 (257)
-+.+..-.|.|..|.+++.|.+.+|+.|... .+.++|+|+...+..|...+. .++..
T Consensus 21 ~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r--------------G~~~~i~g~~~~v~~A~~~l~~l~~~~~ 79 (348)
T COG1702 21 SDDNELVALFGPTDTNLSLLEIALGVSIVAR--------------GEAVRIIGARPLVDVATRVLLTLELLAE 79 (348)
T ss_pred CCchhhhhhcCCCCccHHHHHHHhCcEEEeC--------------CceEEEEechHHHHHHHHHHhHHHHHHH
Confidence 3356678899999999999999999999852 366999999778888877777 55444
No 151
>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=59.22 E-value=7.1 Score=39.03 Aligned_cols=39 Identities=31% Similarity=0.406 Sum_probs=33.9
Q ss_pred EEEEecCcccccccccCchhHHHHHhhhCceEEEccccc
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA 90 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 90 (257)
=.++|-...-|.+|||+|.++++|.++||-+-.|.+..|
T Consensus 95 ~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 95 GEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred ceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 356777888999999999999999999999999887644
No 152
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=58.22 E-value=9.2 Score=33.04 Aligned_cols=32 Identities=22% Similarity=0.427 Sum_probs=26.3
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhCce
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKAT 82 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tga~ 82 (257)
.+++.|....-|.|||++|..|++|+++..-.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~ 76 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKR 76 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHH
Confidence 36777788889999999999999998876443
No 153
>COG1159 Era GTPase [General function prediction only]
Probab=57.22 E-value=12 Score=33.82 Aligned_cols=30 Identities=33% Similarity=0.464 Sum_probs=22.3
Q ss_pred CeEEEEEecCcc-cccccccCchhHHHHHhh
Q 025165 49 DVLFRIIVPSRQ-IGKVIGKEGHRIQKIREE 78 (257)
Q Consensus 49 ~~~~rilVP~~~-vg~IIGkgG~~Ik~I~~~ 78 (257)
.+...|+|+.+. -|-||||+|+.||+|-..
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 355567777654 788999999999988444
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=54.69 E-value=14 Score=31.61 Aligned_cols=28 Identities=32% Similarity=0.536 Sum_probs=22.9
Q ss_pred EEEEeccCccceeecCCChhHHHHHHHh
Q 025165 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 145 ~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
..+.|....-|.+||++|++|+++++.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~L 69 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEIL 69 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHH
Confidence 5666666888999999999999987544
No 155
>CHL00048 rps3 ribosomal protein S3
Probab=53.06 E-value=15 Score=31.54 Aligned_cols=30 Identities=27% Similarity=0.353 Sum_probs=24.7
Q ss_pred eEEEEEeccCccceeecCCChhHHHHHHHh
Q 025165 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 143 ~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
...++.|....-|.|||++|.+|++|++.-
T Consensus 66 ~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 66 DLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 357777888888999999999999987543
No 156
>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=53.06 E-value=16 Score=31.02 Aligned_cols=28 Identities=25% Similarity=0.534 Sum_probs=24.0
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHH
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
..++.|....-|.|||++|..|++|++.
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~ 66 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEK 66 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHH
Confidence 5788888888899999999999988743
No 157
>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=53.00 E-value=41 Score=24.30 Aligned_cols=54 Identities=20% Similarity=0.212 Sum_probs=41.3
Q ss_pred CChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025165 161 SGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (257)
Q Consensus 161 ~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 218 (257)
|=..+.++-+..|++++..-+|.-.- ...+.++++.|+..++..|...++.+|+
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v----~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRV----EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EE----ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCc----cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 44567888888899999765443221 2468999999999999999999988875
No 158
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=50.58 E-value=17 Score=31.41 Aligned_cols=28 Identities=18% Similarity=0.401 Sum_probs=23.6
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHH
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
..++.|....-|.|||++|..|++|++.
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~ 72 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSL 72 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHH
Confidence 4677888888899999999999988743
No 159
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=50.22 E-value=13 Score=31.73 Aligned_cols=34 Identities=26% Similarity=0.460 Sum_probs=29.2
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHhCCeEE
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIV 177 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~ 177 (257)
.+.+-+-.+..+.|||+.|.++..||--+...++
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 5677788888999999999999999988776665
No 160
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=50.13 E-value=14 Score=33.82 Aligned_cols=32 Identities=22% Similarity=0.435 Sum_probs=25.4
Q ss_pred CeEEEEEecCcc-cccccccCchhHHHHHhhhC
Q 025165 49 DVLFRIIVPSRQ-IGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 49 ~~~~rilVP~~~-vg~IIGkgG~~Ik~I~~~tg 80 (257)
.+..+++||... ...||||||..|++|-++.+
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 467889999876 55677999999999976653
No 161
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=46.56 E-value=35 Score=31.32 Aligned_cols=34 Identities=21% Similarity=0.342 Sum_probs=26.0
Q ss_pred CcceEEEEEeccC-ccceeecCCChhHHHHHHHhC
Q 025165 140 VAANTIRLLIAGS-QAGCLIGMSGQNIEKLRNSSG 173 (257)
Q Consensus 140 ~~~~~~~l~Vp~~-~vG~iIGk~G~~Ik~I~~~tg 173 (257)
...+..++.+|.. +...|||++|..|++|-+..+
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 3456778888864 567889999999999976544
No 162
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=45.88 E-value=19 Score=30.81 Aligned_cols=28 Identities=36% Similarity=0.699 Sum_probs=24.3
Q ss_pred EEEEecCcccccccccCchhHHHHHhhh
Q 025165 52 FRIIVPSRQIGKVIGKEGHRIQKIREET 79 (257)
Q Consensus 52 ~rilVP~~~vg~IIGkgG~~Ik~I~~~t 79 (257)
++|.|....-|.|||++|..|++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 6677788888999999999999998765
No 163
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=41.35 E-value=97 Score=25.59 Aligned_cols=59 Identities=20% Similarity=0.269 Sum_probs=43.4
Q ss_pred CcceEEEEEeccCccceeecCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHh
Q 025165 140 VAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (257)
Q Consensus 140 ~~~~~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~ 218 (257)
.+..+.++-++...+- .++.+|.+-.|+-+.+. .+..|.|-|..+.|..|++.+..+-.
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-------------e~~~V~I~Gdke~Ik~aLKe~s~~wk 168 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-------------EDDKVVIEGDKERIKKALKEFSSFWK 168 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEec-------------CCcEEEEeccHHHHHHHHHHHHHHhc
Confidence 3445666666665432 46778889999999871 24569999999999999998876543
No 164
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=39.17 E-value=32 Score=29.47 Aligned_cols=28 Identities=43% Similarity=0.707 Sum_probs=23.3
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHH
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~ 171 (257)
.+++.|....-|.|||++|..|++|++.
T Consensus 63 ~i~I~I~~~~pg~vIG~~g~~i~~l~~~ 90 (211)
T TIGR01009 63 KIRVTIHTARPGIVIGKKGSEIEKLRKD 90 (211)
T ss_pred ceEEEEEeCCCcceeCCCchHHHHHHHH
Confidence 3677788888899999999999998743
No 165
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=37.66 E-value=79 Score=26.40 Aligned_cols=26 Identities=23% Similarity=0.250 Sum_probs=21.3
Q ss_pred eEEEEEc--CHHHHHHHHHHHHHHHhcC
Q 025165 195 RVVQISG--DVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 195 r~V~I~G--~~~~v~~A~~~I~~~l~e~ 220 (257)
..+.||| +++.+++|.+.|...|.+.
T Consensus 155 GK~ViTGaK~~ed~~~Av~~i~~~L~el 182 (185)
T COG2101 155 GKLVITGAKSEEDAEQAVEKIQSRLEEL 182 (185)
T ss_pred CcEEEecCCCHHHHHHHHHHHHHHHHHh
Confidence 3466788 5789999999999999873
No 166
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.11 E-value=1.2e+02 Score=24.48 Aligned_cols=44 Identities=30% Similarity=0.425 Sum_probs=35.1
Q ss_pred hhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 163 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
.++..|.+..|+-|.+. ....|.|-|+.+.|.+|++.|-..-++
T Consensus 126 eRlqDi~E~hgvIiE~~-------------E~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFE-------------EYDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEee-------------eccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 45667778889888873 246799999999999999999877554
No 167
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=36.35 E-value=33 Score=29.85 Aligned_cols=30 Identities=37% Similarity=0.635 Sum_probs=23.9
Q ss_pred EEEEEecCcccccccccCchhHHHHHhhhC
Q 025165 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 51 ~~rilVP~~~vg~IIGkgG~~Ik~I~~~tg 80 (257)
.+.|.|-...-+.|||++|..|++|++...
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 356666667789999999999999987753
No 168
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=34.30 E-value=1.1e+02 Score=23.36 Aligned_cols=41 Identities=24% Similarity=0.169 Sum_probs=32.7
Q ss_pred HHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhcCC
Q 025165 170 NSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (257)
Q Consensus 170 ~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e~~ 221 (257)
+..++.|-+..+ -...+.|+|+-.+|+.|++.+.+.+++..
T Consensus 61 Kaa~V~igF~DR-----------FsGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 61 KAADVHIGFLDR-----------FSGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred hccCcEEeeeec-----------cceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 446788887632 34669999999999999999999998843
No 169
>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=32.97 E-value=1.3e+02 Score=21.10 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=29.7
Q ss_pred ChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025165 162 GQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 162 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
-..|.+|-+.++++|.=.. .+.-+++++|+++.+...++++
T Consensus 16 r~ei~~l~~~f~a~ivd~~-----------~~~~iie~tG~~~kid~fi~~l 56 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS-----------PDSIIIELTGTPEKIDAFIKLL 56 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE-----------TTEEEEEEEE-HHHHHHHHHHS
T ss_pred HHHHHHHHHHhCCEEEEEC-----------CCEEEEEEcCCHHHHHHHHHHh
Confidence 3468888899999997542 3467899999999998666554
No 170
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=28.43 E-value=58 Score=28.34 Aligned_cols=29 Identities=38% Similarity=0.637 Sum_probs=23.2
Q ss_pred EEEEEeccCccceeecCCChhHHHHHHHh
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~~~t 172 (257)
.+++.|....-+.|||++|..|++|++.-
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 46677777778999999999999887543
No 171
>PRK04021 hypothetical protein; Reviewed
Probab=27.37 E-value=1.7e+02 Score=21.65 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=29.7
Q ss_pred hHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEc-CHHHHHHHH
Q 025165 164 NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNAL 210 (257)
Q Consensus 164 ~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G-~~~~v~~A~ 210 (257)
-|+-|.+..|++|.|.+.. .+..++|.|.| +++.+...+
T Consensus 51 li~~LAk~l~~~I~I~~G~--------~sr~K~v~i~g~~~e~l~~~L 90 (92)
T PRK04021 51 LVKFFSKLLGAEVEIIRGE--------TSREKDLLVKGISLEEVKKKL 90 (92)
T ss_pred HHHHHHHHhCCCEEEEecC--------CcCceEEEEecCCHHHHHHHh
Confidence 4677888999999987532 26789999999 777776554
No 172
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=26.06 E-value=73 Score=21.28 Aligned_cols=52 Identities=15% Similarity=0.273 Sum_probs=31.9
Q ss_pred ChhHHH--HHHHhCCeEEEeCCCC---CCcccCCCCCceEEEEEcCHHHHHHHHHHH
Q 025165 162 GQNIEK--LRNSSGATIVILAPNQ---LPLCASAHESDRVVQISGDVPAVLNALVEI 213 (257)
Q Consensus 162 G~~Ik~--I~~~tga~I~i~~~~~---~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I 213 (257)
|.+|++ +++.+++.|.-..++. .|..-..-.....+.|.|+.+.+.++.+++
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 457888 7788888887553321 111000012457899999999998876653
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=24.97 E-value=3.2e+02 Score=24.45 Aligned_cols=56 Identities=14% Similarity=0.097 Sum_probs=43.4
Q ss_pred CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-|-....++-+..|+++++..+|.-.- ...+.++++.|+...+..|...++.+|+-
T Consensus 46 ~G~~~~~~i~~~l~~~~~~~~~dG~~v----~~g~~i~~~~G~a~~ll~~eR~alN~l~~ 101 (277)
T TIGR01334 46 SGVSEAAKLLKQLGASIDYAVPSGSRA----LAGTLLLEAKGSAGQLHQGWKSAQSVLEW 101 (277)
T ss_pred ECHHHHHHHHHHcCCEEEEEeCCCCEe----CCCCEEEEEEecHHHHHHHHHHHHHHHHH
Confidence 345667888888999999876543221 25789999999999999998888877765
No 174
>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=23.98 E-value=1.4e+02 Score=20.90 Aligned_cols=28 Identities=29% Similarity=0.295 Sum_probs=24.7
Q ss_pred CceEEEEEcCHHHHHHHHHHHHHHHhcC
Q 025165 193 SDRVVQISGDVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 193 ~~r~V~I~G~~~~v~~A~~~I~~~l~e~ 220 (257)
..-.+.|+|+..+|+.|++...+.+.+.
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 4678999999999999999999988774
No 175
>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=23.52 E-value=1.5e+02 Score=22.75 Aligned_cols=29 Identities=34% Similarity=0.412 Sum_probs=24.7
Q ss_pred ceEEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 025165 194 DRVVQISGDVPAVLNALVEIGNQLRENPP 222 (257)
Q Consensus 194 ~r~V~I~G~~~~v~~A~~~I~~~l~e~~~ 222 (257)
...+.|+|+..+|+.|++...+.+.+...
T Consensus 73 ~g~vii~GdvsaV~aAl~a~~~~~~~~~~ 101 (110)
T cd07046 73 SGALVITGDVSEVESALEAVVDYLRETLG 101 (110)
T ss_pred eEEEEEEECHHHHHHHHHHHHHHHhhccC
Confidence 34688999999999999999999988543
No 176
>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=23.27 E-value=4.4e+02 Score=26.03 Aligned_cols=68 Identities=16% Similarity=0.243 Sum_probs=40.1
Q ss_pred EEEEEeccCccceeecCCChhHHHHH------HHhCCeEEEeCCCCCCcccCC---CCCceEEEEEcCHHHHHHHHHHHH
Q 025165 144 TIRLLIAGSQAGCLIGMSGQNIEKLR------NSSGATIVILAPNQLPLCASA---HESDRVVQISGDVPAVLNALVEIG 214 (257)
Q Consensus 144 ~~~l~Vp~~~vG~iIGk~G~~Ik~I~------~~tga~I~i~~~~~~p~~~~~---~~~~r~V~I~G~~~~v~~A~~~I~ 214 (257)
...+++|++ .++| .++++++ +.+|+.|.=..+.+..-.... -.....+.+.|++++++++.+.+-
T Consensus 304 ~e~VV~~~S---~liG---kTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 304 TKDVVLTNK---EYNG---KTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEEEEECCc---ccCC---ccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcC
Confidence 445555544 5556 4788886 267888875554321100000 023468999999999998777644
Q ss_pred HHH
Q 025165 215 NQL 217 (257)
Q Consensus 215 ~~l 217 (257)
...
T Consensus 378 ~~~ 380 (562)
T TIGR03802 378 YAI 380 (562)
T ss_pred Cch
Confidence 333
No 177
>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=22.52 E-value=3.7e+02 Score=23.93 Aligned_cols=56 Identities=18% Similarity=0.226 Sum_probs=42.6
Q ss_pred CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCceEEEEEcCHHHHHHHHHHHHHHHhc
Q 025165 160 MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~~l~e 219 (257)
-|-....+|-+..|+++.+.-+|.-.- ...+.++++.|+..++..+...++.+|+-
T Consensus 44 ~G~~~a~~i~~~l~~~~~~~~~dG~~v----~~g~~i~~i~G~a~~ll~~Er~~ln~l~~ 99 (273)
T PRK05848 44 SGEKYALELLEMTGIECVFTIKDGERF----KKGDILMEIEGDFSMLLKVERTLLNLLQH 99 (273)
T ss_pred ECHHHHHHHHHHcCCEEEEEcCCCCEe----cCCCEEEEEEECHHHHHHHHHHHHHHHHH
Confidence 345567888888899888765443211 25789999999999999999888888765
No 178
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=20.69 E-value=1.8e+02 Score=20.69 Aligned_cols=36 Identities=22% Similarity=0.276 Sum_probs=28.4
Q ss_pred hCCeEEEeCCCCCCcccCCCCCceEEEEEc--CHHHHHHHHHHHHHHHhcC
Q 025165 172 SGATIVILAPNQLPLCASAHESDRVVQISG--DVPAVLNALVEIGNQLREN 220 (257)
Q Consensus 172 tga~I~i~~~~~~p~~~~~~~~~r~V~I~G--~~~~v~~A~~~I~~~l~e~ 220 (257)
..+.+.|++ ...|.|+| +.+.+..|...+..+|++.
T Consensus 48 p~~t~~IF~-------------sGki~itGaks~~~~~~a~~~i~~~L~~~ 85 (86)
T PF00352_consen 48 PKATVLIFS-------------SGKIVITGAKSEEEAKKAIEKILPILQKL 85 (86)
T ss_dssp TTEEEEEET-------------TSEEEEEEESSHHHHHHHHHHHHHHHHHT
T ss_pred CcEEEEEEc-------------CCEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 467888874 24577888 6889999999999999863
No 179
>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=20.48 E-value=2.5e+02 Score=19.22 Aligned_cols=53 Identities=17% Similarity=0.172 Sum_probs=35.3
Q ss_pred CCChhHHHHHHHhCCeEEEeCCCC--CCcccCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 025165 160 MSGQNIEKLRNSSGATIVILAPNQ--LPLCASAHESDRVVQISGDVPAVLNALVEIGN 215 (257)
Q Consensus 160 k~G~~Ik~I~~~tga~I~i~~~~~--~p~~~~~~~~~r~V~I~G~~~~v~~A~~~I~~ 215 (257)
....-|.++.+++|..+.|....- +-.. .-..=++.+.|+.+++++|+..+.+
T Consensus 14 ~~~piis~l~~~~~v~~nIl~g~i~~i~~~---~~G~l~l~l~g~~~~~~~a~~~L~~ 68 (76)
T PF09383_consen 14 AQEPIISQLIREFGVDVNILHGNIEEIQGT---PFGILILELPGDDEEIEKAIAYLRE 68 (76)
T ss_dssp SSSCHHHHHHHHHT-EEEEEEEEEEEETTE---EEEEEEEEEES-HHHHHHHHHHHHH
T ss_pred cCchHHHHHHHHhCCCEEEEEEEeEEcCCe---eEEEEEEEEECCHHHHHHHHHHHHH
Confidence 345678999999999999875321 0000 0234588999999999998887765
No 180
>PF03946 Ribosomal_L11_N: Ribosomal protein L11, N-terminal domain; InterPro: IPR020784 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups bacteria, plant chloroplast, red algal chloroplast, cyanelle and archaeabacterial L11; and mammalian, plant and yeast L12 (YL15). L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown [] to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure.; PDB: 2ZJQ_F 2ZJP_F 3CF5_F 2WRJ_K 2WH4_K 2WRL_K 3FIN_L 2X9U_K 3I8I_L 2XUX_K ....
Probab=20.24 E-value=85 Score=21.23 Aligned_cols=29 Identities=24% Similarity=0.492 Sum_probs=22.1
Q ss_pred EEEEecCccc------ccccccCchhHHHHHhhhC
Q 025165 52 FRIIVPSRQI------GKVIGKEGHRIQKIREETK 80 (257)
Q Consensus 52 ~rilVP~~~v------g~IIGkgG~~Ik~I~~~tg 80 (257)
+++.|+...+ |-.+|.-|-+++++.++++
T Consensus 2 i~l~v~aG~A~p~pplgp~LG~~Gin~~~f~k~fN 36 (60)
T PF03946_consen 2 IKLRVPAGKATPAPPLGPALGPLGINIKKFCKDFN 36 (60)
T ss_dssp EEEEEETTSSSSTTTSTHHHHTTTS-HHHHHHHHH
T ss_pred EEEEEecCcccCCCCcCcccccCCCCHHHHHHHHH
Confidence 5667766655 7789999999999988875
No 181
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=20.10 E-value=80 Score=26.03 Aligned_cols=61 Identities=16% Similarity=0.369 Sum_probs=35.5
Q ss_pred cccCchhHHHHHhhhCceEEEccc--cc--------------CCCccEEEecCCCCCchhhHHHHHHHHHHHHHhcC
Q 025165 65 IGKEGHRIQKIREETKATIKIADA--IA--------------RHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (257)
Q Consensus 65 IGkgG~~Ik~I~~~tga~I~i~~~--~~--------------~~~ervv~I~G~~~~~~~~~~~~a~~~I~~~i~~~ 125 (257)
=|+||.+++++-.+..++..+... .+ .....-+.|+...--....++.+|++.|.++|...
T Consensus 50 SGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~~I~~~ 126 (172)
T KOG3429|consen 50 SGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAA 126 (172)
T ss_pred CCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHHHHHHH
Confidence 399999999886555444444321 00 00112266665443222346789999999988654
Done!