Query 021032
Match_columns 318
No_of_seqs 182 out of 1672
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 07:04:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021032.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021032hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2192 PolyC-binding hnRNP-K 100.0 1E-35 2.2E-40 259.4 21.7 273 6-316 98-386 (390)
2 KOG2190 PolyC-binding proteins 100.0 3E-28 6.5E-33 236.2 21.1 279 2-315 100-410 (485)
3 KOG2191 RNA-binding protein NO 100.0 6E-28 1.3E-32 216.3 17.9 167 27-317 38-207 (402)
4 KOG2193 IGF-II mRNA-binding pr 99.9 6.5E-27 1.4E-31 215.4 13.7 225 6-316 256-483 (584)
5 KOG1676 K-homology type RNA bi 99.9 8.6E-25 1.9E-29 210.0 17.0 163 26-314 137-300 (600)
6 KOG1676 K-homology type RNA bi 99.9 7.9E-25 1.7E-29 210.2 16.6 179 7-314 198-389 (600)
7 KOG2190 PolyC-binding proteins 99.9 3.5E-22 7.6E-27 194.0 16.3 159 25-314 40-208 (485)
8 KOG2193 IGF-II mRNA-binding pr 99.8 1E-20 2.2E-25 174.7 9.3 152 27-314 198-352 (584)
9 KOG2192 PolyC-binding hnRNP-K 99.8 4.1E-19 8.9E-24 155.6 12.1 148 25-314 45-193 (390)
10 TIGR03665 arCOG04150 arCOG0415 99.7 1.3E-17 2.7E-22 142.6 12.3 61 32-102 2-65 (172)
11 KOG2191 RNA-binding protein NO 99.7 1.8E-16 3.9E-21 142.8 14.3 203 6-314 94-315 (402)
12 PRK13763 putative RNA-processi 99.7 1.7E-16 3.7E-21 136.5 13.6 65 28-102 3-71 (180)
13 cd02396 PCBP_like_KH K homolog 99.6 2.7E-15 5.8E-20 107.7 6.8 64 246-309 1-65 (65)
14 cd02396 PCBP_like_KH K homolog 99.6 4.1E-15 8.8E-20 106.7 7.4 64 29-96 1-64 (65)
15 PF00013 KH_1: KH domain syndr 99.4 1.3E-13 2.9E-18 97.2 5.6 60 246-308 1-60 (60)
16 cd02394 vigilin_like_KH K homo 99.4 2.3E-13 5E-18 96.6 6.1 61 247-309 2-62 (62)
17 cd00105 KH-I K homology RNA-bi 99.4 7.7E-13 1.7E-17 94.2 7.3 63 247-309 2-64 (64)
18 cd02393 PNPase_KH Polynucleoti 99.4 1.6E-12 3.4E-17 92.0 7.4 59 245-309 2-61 (61)
19 PF00013 KH_1: KH domain syndr 99.4 9.8E-13 2.1E-17 92.7 5.2 60 29-96 1-60 (60)
20 cd02394 vigilin_like_KH K homo 99.4 1.7E-12 3.6E-17 92.2 6.3 60 30-96 2-61 (62)
21 cd02393 PNPase_KH Polynucleoti 99.4 3.5E-12 7.7E-17 90.2 7.9 58 28-96 2-60 (61)
22 cd00105 KH-I K homology RNA-bi 99.3 1.3E-11 2.9E-16 87.7 7.8 63 29-96 1-63 (64)
23 PF13014 KH_3: KH domain 99.2 5.2E-11 1.1E-15 78.1 5.3 43 38-84 1-43 (43)
24 PF13014 KH_3: KH domain 99.1 9.4E-11 2E-15 76.9 5.1 42 255-296 1-43 (43)
25 KOG2279 Kinase anchor protein 99.1 3.9E-11 8.4E-16 115.1 3.8 147 24-315 64-210 (608)
26 smart00322 KH K homology RNA-b 99.1 5.2E-10 1.1E-14 79.7 8.8 66 245-312 3-68 (69)
27 smart00322 KH K homology RNA-b 99.1 1.2E-09 2.7E-14 77.8 8.8 67 27-100 2-68 (69)
28 COG1094 Predicted RNA-binding 98.9 1.3E-08 2.8E-13 86.9 11.6 67 27-103 7-78 (194)
29 cd02395 SF1_like-KH Splicing f 98.7 1E-07 2.2E-12 76.5 8.3 67 37-103 15-96 (120)
30 cd02395 SF1_like-KH Splicing f 98.6 1.3E-07 2.8E-12 75.8 6.9 61 254-314 15-95 (120)
31 TIGR03665 arCOG04150 arCOG0415 98.6 7.8E-08 1.7E-12 82.2 5.4 60 249-313 2-64 (172)
32 PRK13763 putative RNA-processi 98.6 1.7E-07 3.7E-12 80.7 7.0 64 245-313 3-70 (180)
33 KOG2208 Vigilin [Lipid transpo 98.2 4.9E-06 1.1E-10 86.1 9.6 139 28-311 347-485 (753)
34 TIGR02696 pppGpp_PNP guanosine 98.2 6.3E-06 1.4E-10 83.9 10.2 87 5-102 550-642 (719)
35 PRK08406 transcription elongat 98.2 4.9E-06 1.1E-10 68.6 6.6 62 3-64 5-68 (140)
36 KOG2113 Predicted RNA binding 98.1 3.4E-06 7.3E-11 76.4 5.4 65 26-98 24-88 (394)
37 TIGR03591 polynuc_phos polyrib 98.1 1.3E-05 2.8E-10 82.5 8.5 86 6-102 523-615 (684)
38 KOG2279 Kinase anchor protein 98.0 3.4E-05 7.3E-10 74.9 9.8 74 25-103 137-210 (608)
39 TIGR02696 pppGpp_PNP guanosine 97.9 2.3E-05 5E-10 79.9 7.3 64 244-313 577-641 (719)
40 TIGR01952 nusA_arch NusA famil 97.8 9.7E-05 2.1E-09 60.9 7.2 62 3-64 5-69 (141)
41 KOG0119 Splicing factor 1/bran 97.8 9.8E-05 2.1E-09 71.0 8.2 76 27-102 137-230 (554)
42 KOG2208 Vigilin [Lipid transpo 97.7 0.00015 3.2E-09 75.3 9.8 70 244-315 346-415 (753)
43 PLN00207 polyribonucleotide nu 97.7 7.3E-05 1.6E-09 77.9 7.2 87 5-102 656-750 (891)
44 KOG1588 RNA-binding protein Sa 97.7 0.00028 6E-09 63.1 9.5 81 26-106 90-191 (259)
45 KOG0119 Splicing factor 1/bran 97.6 0.00016 3.5E-09 69.5 7.7 72 244-315 137-231 (554)
46 TIGR03591 polynuc_phos polyrib 97.6 0.0001 2.2E-09 76.0 6.6 65 244-314 550-615 (684)
47 TIGR03319 YmdA_YtgF conserved 97.4 0.00041 8.9E-09 69.1 7.7 69 243-316 202-272 (514)
48 PRK00106 hypothetical protein; 97.4 0.00045 9.7E-09 68.8 7.8 69 243-316 223-293 (535)
49 KOG2814 Transcription coactiva 97.4 0.00023 4.9E-09 65.5 5.2 71 27-103 56-126 (345)
50 KOG0336 ATP-dependent RNA heli 97.4 0.00015 3.3E-09 68.7 4.2 69 25-101 44-112 (629)
51 KOG0336 ATP-dependent RNA heli 97.4 0.00019 4.2E-09 68.0 4.6 68 244-314 46-113 (629)
52 PRK11824 polynucleotide phosph 97.4 0.00029 6.3E-09 72.7 6.2 87 5-102 525-618 (693)
53 COG1185 Pnp Polyribonucleotide 97.4 0.00064 1.4E-08 68.3 8.2 87 6-103 524-617 (692)
54 PRK12704 phosphodiesterase; Pr 97.3 0.00072 1.6E-08 67.5 7.5 69 243-316 208-278 (520)
55 cd02134 NusA_KH NusA_K homolog 97.2 0.00054 1.2E-08 48.2 4.6 37 27-63 24-60 (61)
56 COG1094 Predicted RNA-binding 97.2 0.001 2.2E-08 57.1 6.5 54 38-103 112-165 (194)
57 PRK04163 exosome complex RNA-b 97.2 0.001 2.2E-08 59.8 6.7 65 247-317 147-212 (235)
58 cd02134 NusA_KH NusA_K homolog 97.1 0.00063 1.4E-08 47.8 3.9 36 245-280 25-60 (61)
59 PLN00207 polyribonucleotide nu 97.1 0.00065 1.4E-08 71.0 5.1 65 244-314 684-750 (891)
60 COG1185 Pnp Polyribonucleotide 97.0 0.0012 2.7E-08 66.3 5.7 65 244-314 551-616 (692)
61 COG0195 NusA Transcription elo 96.8 0.002 4.4E-08 55.7 5.0 37 246-282 143-179 (190)
62 COG5176 MSL5 Splicing factor ( 96.7 0.0037 8.1E-08 53.9 6.0 78 26-103 146-241 (269)
63 KOG2814 Transcription coactiva 96.7 0.0024 5.1E-08 58.9 5.1 71 244-316 56-127 (345)
64 PRK00468 hypothetical protein; 96.7 0.0019 4.1E-08 47.3 3.4 33 24-56 26-58 (75)
65 COG1837 Predicted RNA-binding 96.6 0.0044 9.6E-08 45.3 5.1 33 24-56 26-58 (76)
66 KOG1588 RNA-binding protein Sa 96.6 0.0027 5.8E-08 56.9 4.3 39 243-281 90-134 (259)
67 PRK12705 hypothetical protein; 96.5 0.004 8.8E-08 61.7 5.3 68 244-316 197-266 (508)
68 PRK01064 hypothetical protein; 96.4 0.0079 1.7E-07 44.4 5.4 33 24-56 26-58 (78)
69 KOG4369 RTK signaling protein 96.4 0.00085 1.9E-08 70.3 0.3 73 242-314 1337-1410(2131)
70 PRK04163 exosome complex RNA-b 96.4 0.0066 1.4E-07 54.5 5.9 63 30-103 147-210 (235)
71 PRK02821 hypothetical protein; 96.3 0.0077 1.7E-07 44.3 4.8 33 24-56 27-59 (77)
72 PRK00468 hypothetical protein; 96.3 0.004 8.7E-08 45.6 3.3 31 244-274 29-59 (75)
73 PF14611 SLS: Mitochondrial in 96.2 0.43 9.2E-06 41.9 16.4 65 29-103 27-91 (210)
74 PRK11824 polynucleotide phosph 96.2 0.0043 9.3E-08 64.2 4.0 64 245-314 554-618 (693)
75 PRK02821 hypothetical protein; 96.2 0.0052 1.1E-07 45.2 3.2 33 244-276 30-62 (77)
76 COG5176 MSL5 Splicing factor ( 96.1 0.012 2.6E-07 50.9 5.2 39 244-282 147-191 (269)
77 TIGR01953 NusA transcription t 96.0 0.017 3.6E-07 54.7 6.7 38 245-282 301-338 (341)
78 PRK12328 nusA transcription el 96.0 0.013 2.7E-07 55.8 5.7 38 245-282 308-345 (374)
79 COG1837 Predicted RNA-binding 95.6 0.013 2.9E-07 42.8 3.3 32 243-274 28-59 (76)
80 PRK12327 nusA transcription el 95.6 0.03 6.5E-07 53.4 6.5 38 245-282 303-340 (362)
81 PRK01064 hypothetical protein; 95.5 0.012 2.6E-07 43.5 2.6 32 243-274 28-59 (78)
82 PRK09202 nusA transcription el 95.4 0.042 9.1E-07 54.2 6.9 38 245-282 302-339 (470)
83 PRK12704 phosphodiesterase; Pr 95.3 0.076 1.6E-06 53.2 8.7 49 26-84 208-257 (520)
84 KOG2113 Predicted RNA binding 95.3 0.014 2.9E-07 53.5 3.0 65 243-310 24-88 (394)
85 KOG3273 Predicted RNA-binding 95.3 0.01 2.2E-07 51.0 2.0 64 28-103 169-232 (252)
86 TIGR03319 YmdA_YtgF conserved 95.3 0.086 1.9E-06 52.8 8.8 50 25-84 201-251 (514)
87 PRK12329 nusA transcription el 95.1 0.053 1.2E-06 52.6 6.6 38 245-282 335-372 (449)
88 PRK00106 hypothetical protein; 95.1 0.12 2.6E-06 51.8 9.2 50 25-84 222-272 (535)
89 PF13184 KH_5: NusA-like KH do 94.8 0.026 5.7E-07 40.6 2.7 36 30-65 5-46 (69)
90 KOG1067 Predicted RNA-binding 94.3 0.11 2.4E-06 51.4 6.5 86 6-103 569-661 (760)
91 cd02409 KH-II KH-II (K homolo 94.2 0.089 1.9E-06 36.8 4.3 35 27-61 24-58 (68)
92 PRK08406 transcription elongat 93.9 0.076 1.7E-06 43.8 4.1 38 245-282 32-69 (140)
93 KOG1067 Predicted RNA-binding 93.5 0.25 5.5E-06 49.0 7.4 65 245-316 597-662 (760)
94 PF13083 KH_4: KH domain; PDB: 93.5 0.033 7.2E-07 40.4 1.1 34 25-58 26-59 (73)
95 PF07650 KH_2: KH domain syndr 93.5 0.038 8.2E-07 40.6 1.3 35 28-62 25-59 (78)
96 PF13083 KH_4: KH domain; PDB: 92.9 0.066 1.4E-06 38.8 1.8 33 244-276 28-60 (73)
97 COG1097 RRP4 RNA-binding prote 92.2 0.28 6.1E-06 43.7 5.2 58 247-310 148-206 (239)
98 KOG3273 Predicted RNA-binding 92.0 0.1 2.2E-06 45.0 2.2 53 254-313 178-230 (252)
99 PRK12705 hypothetical protein; 92.0 0.37 8E-06 48.0 6.4 39 26-64 196-235 (508)
100 cd02409 KH-II KH-II (K homolo 91.9 0.27 5.8E-06 34.3 4.0 34 245-278 25-58 (68)
101 PRK13764 ATPase; Provisional 91.7 0.29 6.3E-06 49.8 5.4 44 27-70 480-523 (602)
102 cd02414 jag_KH jag_K homology 91.5 0.22 4.8E-06 36.5 3.3 33 29-61 25-57 (77)
103 PF13184 KH_5: NusA-like KH do 91.4 0.21 4.6E-06 35.9 3.0 36 247-282 5-46 (69)
104 COG1855 ATPase (PilT family) [ 91.2 0.21 4.6E-06 48.6 3.6 38 29-66 487-524 (604)
105 cd02413 40S_S3_KH K homology R 91.1 0.27 5.9E-06 36.5 3.4 36 28-63 30-65 (81)
106 TIGR01952 nusA_arch NusA famil 91.1 0.26 5.6E-06 40.7 3.6 37 246-282 34-70 (141)
107 KOG4369 RTK signaling protein 90.8 0.063 1.4E-06 57.0 -0.3 69 30-102 1342-1410(2131)
108 PRK06418 transcription elongat 90.6 0.29 6.4E-06 41.4 3.5 34 30-64 63-96 (166)
109 PF07650 KH_2: KH domain syndr 90.6 0.19 4E-06 36.8 2.1 34 245-278 25-58 (78)
110 PRK12328 nusA transcription el 89.7 0.55 1.2E-05 44.8 4.9 43 27-69 307-349 (374)
111 TIGR01953 NusA transcription t 89.5 0.41 8.8E-06 45.4 4.0 39 28-66 301-339 (341)
112 COG1855 ATPase (PilT family) [ 88.6 0.35 7.6E-06 47.2 2.8 39 244-282 485-523 (604)
113 PRK13764 ATPase; Provisional 88.3 0.46 1E-05 48.4 3.6 40 243-282 479-518 (602)
114 COG0195 NusA Transcription elo 88.2 0.46 9.9E-06 41.2 3.1 37 29-65 143-179 (190)
115 COG1097 RRP4 RNA-binding prote 88.2 1.2 2.7E-05 39.7 5.8 45 32-87 150-194 (239)
116 PF14611 SLS: Mitochondrial in 87.6 2.7 5.8E-05 36.8 7.7 65 246-315 27-91 (210)
117 cd02411 archeal_30S_S3_KH K ho 87.5 0.66 1.4E-05 34.7 3.2 28 30-57 40-67 (85)
118 cd02414 jag_KH jag_K homology 87.4 0.67 1.5E-05 33.9 3.2 35 245-279 24-58 (77)
119 cd02410 archeal_CPSF_KH The ar 87.0 1.1 2.4E-05 37.0 4.4 38 29-66 77-114 (145)
120 cd02412 30S_S3_KH K homology R 87.0 0.6 1.3E-05 36.7 2.8 30 29-58 62-91 (109)
121 KOG2874 rRNA processing protei 86.0 1.6 3.5E-05 39.7 5.3 52 257-315 161-212 (356)
122 cd02413 40S_S3_KH K homology R 84.5 1.1 2.3E-05 33.3 3.0 36 245-280 30-65 (81)
123 PRK12327 nusA transcription el 84.2 1.2 2.6E-05 42.6 3.9 40 27-66 302-341 (362)
124 COG0092 RpsC Ribosomal protein 84.2 1 2.2E-05 40.1 3.2 37 27-63 50-91 (233)
125 PRK09202 nusA transcription el 84.1 0.93 2E-05 44.9 3.2 39 28-66 302-340 (470)
126 cd02410 archeal_CPSF_KH The ar 83.1 1.3 2.9E-05 36.4 3.3 42 244-285 75-116 (145)
127 KOG2874 rRNA processing protei 82.5 2.9 6.3E-05 38.1 5.4 51 40-102 161-211 (356)
128 TIGR00436 era GTP-binding prot 82.2 1.8 3.9E-05 39.4 4.1 30 27-56 220-250 (270)
129 PRK12329 nusA transcription el 80.7 1.5 3.2E-05 42.9 3.1 38 28-65 335-372 (449)
130 PRK06418 transcription elongat 78.5 3.5 7.6E-05 34.9 4.4 36 246-282 62-97 (166)
131 cd02412 30S_S3_KH K homology R 78.4 2 4.3E-05 33.7 2.7 29 247-275 63-91 (109)
132 PRK15494 era GTPase Era; Provi 77.9 2.9 6.2E-05 39.6 4.1 36 28-63 273-317 (339)
133 COG1782 Predicted metal-depend 77.9 7.8 0.00017 38.5 7.0 39 28-66 99-137 (637)
134 PRK00089 era GTPase Era; Revie 77.9 2.9 6.3E-05 38.4 4.1 36 28-63 226-270 (292)
135 cd02411 archeal_30S_S3_KH K ho 77.9 2.2 4.8E-05 31.8 2.7 28 247-274 40-67 (85)
136 COG1782 Predicted metal-depend 76.8 12 0.00025 37.3 7.9 41 245-285 99-139 (637)
137 COG1159 Era GTPase [General fu 75.1 4 8.7E-05 37.8 4.1 37 27-63 228-273 (298)
138 COG1847 Jag Predicted RNA-bind 71.2 8.2 0.00018 33.8 4.9 70 27-104 90-160 (208)
139 KOG1423 Ras-like GTPase ERA [C 70.5 5 0.00011 37.5 3.5 33 26-58 326-359 (379)
140 COG0092 RpsC Ribosomal protein 70.0 3.9 8.4E-05 36.4 2.7 29 245-273 51-79 (233)
141 TIGR01008 rpsC_E_A ribosomal p 69.6 5.2 0.00011 34.8 3.4 31 27-57 37-67 (195)
142 PRK04191 rps3p 30S ribosomal p 68.1 5.7 0.00012 34.9 3.3 29 30-58 42-70 (207)
143 PTZ00084 40S ribosomal protein 67.6 5.6 0.00012 35.3 3.2 30 28-57 44-73 (220)
144 CHL00048 rps3 ribosomal protei 67.3 6 0.00013 35.0 3.3 31 27-57 65-95 (214)
145 TIGR03675 arCOG00543 arCOG0054 63.9 12 0.00025 38.7 5.1 39 28-66 93-131 (630)
146 TIGR00436 era GTP-binding prot 61.9 8.3 0.00018 35.0 3.3 30 245-274 221-251 (270)
147 PRK15494 era GTPase Era; Provi 57.0 11 0.00024 35.7 3.3 30 245-274 273-303 (339)
148 COG1702 PhoH Phosphate starvat 56.7 32 0.00068 32.7 6.2 51 252-309 22-72 (348)
149 PRK00089 era GTPase Era; Revie 56.2 12 0.00025 34.4 3.3 30 245-274 226-256 (292)
150 PF02749 QRPTase_N: Quinolinat 55.7 47 0.001 24.7 6.0 65 245-313 18-85 (88)
151 COG1159 Era GTPase [General fu 54.0 14 0.00029 34.3 3.3 31 244-274 228-259 (298)
152 TIGR03675 arCOG00543 arCOG0054 53.9 8.7 0.00019 39.6 2.2 42 244-285 92-133 (630)
153 PF09869 DUF2096: Uncharacteri 53.4 40 0.00086 28.5 5.6 41 48-99 126-166 (169)
154 TIGR01009 rpsC_bact ribosomal 53.1 14 0.0003 32.6 3.1 27 30-56 64-90 (211)
155 KOG1423 Ras-like GTPase ERA [C 52.0 13 0.00028 34.8 2.8 33 244-276 327-360 (379)
156 COG1847 Jag Predicted RNA-bind 51.7 14 0.00031 32.3 2.9 69 245-316 91-165 (208)
157 TIGR01008 rpsC_E_A ribosomal p 49.5 16 0.00034 31.9 2.8 29 246-274 39-67 (195)
158 PRK04191 rps3p 30S ribosomal p 49.1 15 0.00033 32.3 2.7 30 247-276 42-71 (207)
159 CHL00048 rps3 ribosomal protei 47.4 18 0.00038 32.0 2.9 29 246-274 67-95 (214)
160 PTZ00084 40S ribosomal protein 45.3 19 0.0004 32.1 2.6 29 246-274 45-73 (220)
161 PRK00310 rpsC 30S ribosomal pr 41.1 26 0.00056 31.4 2.9 30 28-57 62-91 (232)
162 PRK15468 carboxysome structura 40.8 78 0.0017 24.8 5.1 28 77-104 74-101 (111)
163 COG4010 Uncharacterized protei 39.7 85 0.0018 26.0 5.4 43 48-101 126-168 (170)
164 COG5166 Uncharacterized conser 39.7 23 0.00049 35.3 2.5 74 27-103 448-525 (657)
165 TIGR01009 rpsC_bact ribosomal 34.7 35 0.00076 30.1 2.7 28 247-274 64-91 (211)
166 PF02080 TrkA_C: TrkA-C domain 33.6 52 0.0011 22.7 3.1 49 47-95 14-69 (71)
167 PF02749 QRPTase_N: Quinolinat 31.9 1.5E+02 0.0032 21.9 5.4 71 25-101 15-85 (88)
168 COG1702 PhoH Phosphate starvat 31.8 1.5E+02 0.0032 28.3 6.4 53 33-97 20-72 (348)
169 PF03958 Secretin_N: Bacterial 30.6 63 0.0014 23.1 3.2 33 274-311 44-76 (82)
170 PF00936 BMC: BMC domain; Int 25.7 1.3E+02 0.0029 21.5 4.1 28 76-103 38-65 (75)
171 COG3140 Uncharacterized protei 25.1 99 0.0021 21.1 2.9 22 297-318 9-30 (60)
172 PRK06106 nicotinate-nucleotide 24.7 5.6E+02 0.012 23.7 8.9 74 26-101 27-110 (281)
173 PRK00310 rpsC 30S ribosomal pr 24.4 72 0.0016 28.6 2.9 29 246-274 63-91 (232)
174 PF09383 NIL: NIL domain; Int 23.3 1.7E+02 0.0037 20.7 4.3 52 47-98 16-68 (76)
175 cd07049 BMC_EutL_repeat1 ethan 23.0 1.7E+02 0.0038 22.7 4.4 29 287-315 71-100 (103)
176 cd07055 BMC_like_2 Bacterial M 22.0 1E+02 0.0022 21.6 2.6 21 78-98 39-59 (61)
177 COG5166 Uncharacterized conser 20.5 54 0.0012 32.8 1.4 38 246-283 450-487 (657)
No 1
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1e-35 Score=259.41 Aligned_cols=273 Identities=22% Similarity=0.362 Sum_probs=176.9
Q ss_pred HHHHHHHHHHHHHhh---ccCCCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEE
Q 021032 6 AQDAVMRVHSRIAEI---GFEPGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV 82 (318)
Q Consensus 6 a~~a~~~v~~~i~~~---~~e~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I 82 (318)
..+-+..|+..|+-. ++...+++++||||+.+++|.|||++|++||+|||++.|+++|... ||+.++||+|.|
T Consensus 98 d~~ti~~ilk~iip~lee~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~----c~p~stdrv~l~ 173 (390)
T KOG2192|consen 98 DIETIGEILKKIIPTLEEGFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE----CCPHSTDRVVLI 173 (390)
T ss_pred cHHHHHHHHHHHhhhhhhCCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc----cCCCCcceEEEe
Confidence 344555555555543 3446788999999999999999999999999999999999999977 999999999999
Q ss_pred EecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 83 IGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPF 162 (318)
Q Consensus 83 ~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~ 162 (318)
.|++.+|..+++.|++.|.|. +++.++.+|+|.|.+ +.+.|... ..+.+..+.. ....+.+.
T Consensus 174 ~g~~k~v~~~i~~il~~i~e~------pikgsa~py~p~fyd-~t~dyggf---------~M~f~d~pg~--pgpapqrg 235 (390)
T KOG2192|consen 174 GGKPKRVVECIKIILDLISES------PIKGSAQPYDPNFYD-ETYDYGGF---------TMMFDDRPGR--PGPAPQRG 235 (390)
T ss_pred cCCcchHHHHHHHHHHHhhcC------CcCCcCCcCCccccC-cccccCCc---------eeecCCCCCC--CCCCCCCC
Confidence 999999999999999999997 788899999999843 22222111 0000000000 00000000
Q ss_pred CCcccccCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCC----CCC-----CCCCCCCC-CCCCCCCCCCCCCCCCCCC
Q 021032 163 DHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHG---PTFD----RPP-----SPRSWTPQ-GVGGGDPRGFDASSGFTPR 229 (318)
Q Consensus 163 ~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~---~~~~----~~~-----~~~~~~~~-~~~~~~~~g~~~~~~~~~~ 229 (318)
|-++-+++..+...+..++..+... .+|. .|. .|..|.+. ..-+++.+.+.....+.+.
T Consensus 236 --------gqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsY 307 (390)
T KOG2192|consen 236 --------GQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSY 307 (390)
T ss_pred --------CCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCcccccccccc
Confidence 0000000111111111111000000 0111 011 22333211 1101111111111101100
Q ss_pred CCCCCCCCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032 230 NRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 309 (318)
Q Consensus 230 ~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~ 309 (318)
.++ .....|.+|.||.++-|.||||+|.+|++|++++||+|+|+++.+++.||+++|+||.+|++.||+|++
T Consensus 308 -Gdl-------GGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQ 379 (390)
T KOG2192|consen 308 -GDL-------GGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQ 379 (390)
T ss_pred -CCC-------CCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHH
Confidence 111 124678999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCc
Q 021032 310 AFILCGV 316 (318)
Q Consensus 310 ~~i~~~~ 316 (318)
++|+.++
T Consensus 380 n~Vkq~r 386 (390)
T KOG2192|consen 380 NSVKQYR 386 (390)
T ss_pred HHHHhhh
Confidence 9998754
No 2
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=3e-28 Score=236.21 Aligned_cols=279 Identities=25% Similarity=0.293 Sum_probs=169.2
Q ss_pred CCChHHHHHHHHHHHHHhhcc------C------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCC
Q 021032 2 RHSPAQDAVMRVHSRIAEIGF------E------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA 69 (318)
Q Consensus 2 ~~s~a~~a~~~v~~~i~~~~~------e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~ 69 (318)
.+|++++|++++|++|....+ + +..++++|||||++++|+||||+|++||+|+|+|||+|+|++. ++
T Consensus 100 ~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~l 178 (485)
T KOG2190|consen 100 NLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-ML 178 (485)
T ss_pred cCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CC
Confidence 468999999999999998521 1 1225899999999999999999999999999999999999854 88
Q ss_pred CCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 70 PRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPF 149 (318)
Q Consensus 70 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~ 149 (318)
|.| ++|.|+|.|++++|.+|+..|+.+|+++.-. ..+...++.+|.|+.++.-+.... ++..
T Consensus 179 P~s---ter~V~IsG~~~av~~al~~Is~~L~~~~~~-~~~~~~st~~y~P~~~~~~~~~~s--------------~~~~ 240 (485)
T KOG2190|consen 179 PNS---TERAVTISGEPDAVKKALVQISSRLLENPPR-SPPPLVSTIPYRPSASQGGPVLPS--------------TAQT 240 (485)
T ss_pred Ccc---cceeEEEcCchHHHHHHHHHHHHHHHhcCCc-CCCCCCCcccCCCcccccCccccc--------------cccC
Confidence 874 8999999999999999999999999997311 112344666777621110000000 0000
Q ss_pred CCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCC-CCCCCCCCCCCCCCCC
Q 021032 150 HSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDR-----PPSPRSW-TPQGVGGGDPRGFDAS 223 (318)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~-----~~~~~~~-~~~~~~~~~~~g~~~~ 223 (318)
.. +..++......++. ..... .|....+...|-+..... ....... .+.......... .
T Consensus 241 ~~-~~~~~~~~~~~~e~----~~~~~-------~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~---~ 305 (485)
T KOG2190|consen 241 SP-DAHPFGGIVPEEEL----VFKLI-------CPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTDRIVTISA---R 305 (485)
T ss_pred Cc-ccccccccccchhh----hhhhc-------CchhhceeeecCCCccchhhhhhcCCceEeccccCcceeeecc---c
Confidence 00 00000000000000 00000 000000000000000000 0000000 000000000000 0
Q ss_pred CCCCCC----CCCC--------CCCCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC--CCCC
Q 021032 224 SGFTPR----NRPV--------ESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP--GATE 289 (318)
Q Consensus 224 ~~~~~~----~~~~--------~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~--~~~e 289 (318)
....++ ...+ ......+ ...++.++.||.+++|+||||+|++|.+||+.|||.|+|.+... ...|
T Consensus 306 e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~~~~~e 384 (485)
T KOG2190|consen 306 ENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEVSGVRE 384 (485)
T ss_pred cCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEccccccCCcce
Confidence 000000 0000 0001111 34588999999999999999999999999999999999998776 8899
Q ss_pred eEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032 290 GVVMVSGTSDQMRAAQSLIHAFILCG 315 (318)
Q Consensus 290 r~v~I~Gt~~~v~~A~~lI~~~i~~~ 315 (318)
+.++|+|+..+...|++++..++...
T Consensus 385 ~~~~I~~~~~~~~~~~~~~~~~~~~~ 410 (485)
T KOG2190|consen 385 ALVQITGMLREDLLAQYLIRARLSAP 410 (485)
T ss_pred eEEEecchhHHHHhhhhhcccccccC
Confidence 99999999999999999998887764
No 3
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=6e-28 Score=216.26 Aligned_cols=167 Identities=23% Similarity=0.376 Sum_probs=137.8
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCC
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP 106 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~ 106 (318)
.+.+|+|||+..+|+||||||++|.+||.+|||+|++++..+ +|++.+||+|.|+|+.+++......|.++|||....
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~d--fyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~ 115 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKD--FYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQA 115 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccc--cCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHh
Confidence 499999999999999999999999999999999999986443 777899999999999999999999999999997321
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 021032 107 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP 186 (318)
Q Consensus 107 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 186 (318)
... +..+|.
T Consensus 116 ~~k----------------~v~~~~------------------------------------------------------- 124 (402)
T KOG2191|consen 116 VAK----------------PVDILQ------------------------------------------------------- 124 (402)
T ss_pred hcC----------------CccccC-------------------------------------------------------
Confidence 100 000000
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccch
Q 021032 187 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN 266 (318)
Q Consensus 187 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~ 266 (318)
++.. ......++.+|++.+|.||||+|++
T Consensus 125 ----------------------pqt~-----------------------------~r~kqikivvPNstag~iigkggAt 153 (402)
T KOG2191|consen 125 ----------------------PQTP-----------------------------DRIKQIKIVVPNSTAGMIIGKGGAT 153 (402)
T ss_pred ----------------------CCCc-----------------------------cccceeEEeccCCcccceecCCcch
Confidence 0000 0123488999999999999999999
Q ss_pred HHHHHHHhCCEEEEcCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHHHcCcC
Q 021032 267 LSHIRQISGANVVVNDPKP---GATEGVVMVSGTSDQMRAAQSLIHAFILCGVT 317 (318)
Q Consensus 267 Ik~Ir~~SGA~I~i~~~~~---~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~~ 317 (318)
||.|++++||.|+|+...+ .-.||.|+++|++|+..+|..||.++|.++..
T Consensus 154 iK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 154 IKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred HHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 9999999999999984332 45799999999999999999999999998754
No 4
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=6.5e-27 Score=215.35 Aligned_cols=225 Identities=19% Similarity=0.306 Sum_probs=156.1
Q ss_pred HHHHHHHHHHHHHhhccC--CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEE
Q 021032 6 AQDAVMRVHSRIAEIGFE--PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI 83 (318)
Q Consensus 6 a~~a~~~v~~~i~~~~~e--~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~ 83 (318)
+..|+..|++-|..+..+ -.+.+.||+|-++++||.||||.|.+||+|+.+||++|.|++-.++..| ..||.++|.
T Consensus 256 ~s~Ac~~ILeimqkEA~~~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y--npERTItVk 333 (584)
T KOG2193|consen 256 TSKACKMILEIMQKEAVDDKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY--NPERTITVK 333 (584)
T ss_pred hHHHHHHHHHHHHHhhhccchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc--CccceEEec
Confidence 345666666665544322 2478899999999999999999999999999999999999986666555 679999999
Q ss_pred ecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 84 GNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFD 163 (318)
Q Consensus 84 G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~ 163 (318)
|..|+|.+|..+|+.+|+|+...+ ....+..+.+.| +.....++.|++. |++
T Consensus 334 GsiEac~~AE~eImkKlre~yEnD-l~a~s~q~~l~P-------------------~l~~~~l~~f~ss--S~~------ 385 (584)
T KOG2193|consen 334 GSIEACVQAEAEIMKKLRECYEND-LAAMSLQCHLPP-------------------GLNLPALGLFPSS--SAV------ 385 (584)
T ss_pred ccHHHHHHHHHHHHHHHHHHHhhh-HHHhhccCCCCc-------------------ccCccccCCCCcc--ccc------
Confidence 999999999999999999974322 222221111111 1111111111110 000
Q ss_pred CcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCc
Q 021032 164 HQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILT 243 (318)
Q Consensus 164 ~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~ 243 (318)
.+ |.| +|..+.+..+ ++ .... ..+
T Consensus 386 ------------~~------------------Ph~---------~Ps~v~~a~p--------~~-------~~hq--~pe 409 (584)
T KOG2193|consen 386 ------------SP------------------PHF---------PPSPVTFASP--------YP-------LFHQ--NPE 409 (584)
T ss_pred ------------CC------------------CCC---------CCCccccCCC--------ch-------hhhc--Ccc
Confidence 00 000 0000000000 00 0000 124
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC-CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcCc
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~-~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~~ 316 (318)
..++++.||...+|+||||+|.+||+|.+.+||+|+|..+ .++..||+|+|+|.+++.-+||..|..+|+++-
T Consensus 410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhc
Confidence 5678999999999999999999999999999999999865 467899999999999999999999999998753
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.93 E-value=8.6e-25 Score=209.97 Aligned_cols=163 Identities=21% Similarity=0.333 Sum_probs=134.7
Q ss_pred CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcC
Q 021032 26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIF 105 (318)
Q Consensus 26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~ 105 (318)
..++..++||.+.+|+||||+|++||.|+|+|||++.+........ ..++.+.|+|+++.|+.|..+|.++|+|..
T Consensus 137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp~~ve~a~~lV~dil~e~~- 212 (600)
T KOG1676|consen 137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDPDKVEQAKQLVADILREED- 212 (600)
T ss_pred cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCHHHHHHHHHHHHHHHHhcc-
Confidence 3489999999999999999999999999999999999987654432 478999999999999999999999999741
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCC
Q 021032 106 PMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPF 185 (318)
Q Consensus 106 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~ 185 (318)
+.. + .+.+ |
T Consensus 213 -~~~--------------------~------g~~~-----------------------------~--------------- 221 (600)
T KOG1676|consen 213 -DEV--------------------P------GSGG-----------------------------H--------------- 221 (600)
T ss_pred -cCC--------------------C------cccc-----------------------------c---------------
Confidence 100 0 0000 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccc
Q 021032 186 PYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNS 265 (318)
Q Consensus 186 ~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~ 265 (318)
+|. + .....+.+|.||.+.||.||||+|+
T Consensus 222 -~g~-------------------------------~-------------------~g~~~~~~V~VPr~~VG~IIGkgGE 250 (600)
T KOG1676|consen 222 -AGV-------------------------------R-------------------GGGSATREVKVPRSKVGIIIGKGGE 250 (600)
T ss_pred -cCc-------------------------------C-------------------ccccceeEEeccccceeeEEecCch
Confidence 000 0 0112489999999999999999999
Q ss_pred hHHHHHHHhCCEEEEcCCCC-CCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032 266 NLSHIRQISGANVVVNDPKP-GATEGVVMVSGTSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 266 ~Ik~Ir~~SGA~I~i~~~~~-~~~er~v~I~Gt~~~v~~A~~lI~~~i~~ 314 (318)
+||+|+.+||++|+|..+.+ .+.||++.|.|++++|+.|..||.++|++
T Consensus 251 ~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 251 MIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE 300 (600)
T ss_pred HHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence 99999999999999976544 78999999999999999999999999986
No 6
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.93 E-value=7.9e-25 Score=210.23 Aligned_cols=179 Identities=22% Similarity=0.312 Sum_probs=142.6
Q ss_pred HHHHHHHHHHHHhhccC-----------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCC
Q 021032 7 QDAVMRVHSRIAEIGFE-----------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSP 75 (318)
Q Consensus 7 ~~a~~~v~~~i~~~~~e-----------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~ 75 (318)
+.|-.+|++-|.|...+ .....+++|.||.+.||.||||+|++||+|+.+||+||+|.+ |+.| ++
T Consensus 198 e~a~~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p---~s 273 (600)
T KOG1676|consen 198 EQAKQLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDP---SS 273 (600)
T ss_pred HHHHHHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCC---CC
Confidence 34556666666654332 123458999999999999999999999999999999999975 4444 47
Q ss_pred CCceEEEEecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 76 HDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRG 155 (318)
Q Consensus 76 ~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~ 155 (318)
.||.+.|.|.+++|..|..+|.++|.+...- + ..+|+
T Consensus 274 peR~~~IiG~~d~ie~Aa~lI~eii~~~~~~--------------------------~---------~~~~~-------- 310 (600)
T KOG1676|consen 274 PERPAQIIGTVDQIEHAAELINEIIAEAEAG--------------------------A---------GGGMG-------- 310 (600)
T ss_pred ccceeeeecCHHHHHHHHHHHHHHHHHHhcc--------------------------C---------CCCcC--------
Confidence 8999999999999999999999999986100 0 00000
Q ss_pred CCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 156 MGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVES 235 (318)
Q Consensus 156 ~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 235 (318)
| | .
T Consensus 311 ---------------------------------------------------~-----------G------~--------- 313 (600)
T KOG1676|consen 311 ---------------------------------------------------G-----------G------A--------- 313 (600)
T ss_pred ---------------------------------------------------C-----------C------C---------
Confidence 0 0 0
Q ss_pred CCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCC--CCCCCCeEEEEEcCHHHHHHHHHHHHHHHH
Q 021032 236 GNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP--KPGATEGVVMVSGTSDQMRAAQSLIHAFIL 313 (318)
Q Consensus 236 ~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~--~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~ 313 (318)
......+++.||.+.+|.||||+|++||.|.++|||++.+... ..+..||+++|+|++.||.-|+.||+++|.
T Consensus 314 -----P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg 388 (600)
T KOG1676|consen 314 -----PGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVG 388 (600)
T ss_pred -----ccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhc
Confidence 0001268999999999999999999999999999999999865 346789999999999999999999999986
Q ss_pred c
Q 021032 314 C 314 (318)
Q Consensus 314 ~ 314 (318)
.
T Consensus 389 ~ 389 (600)
T KOG1676|consen 389 D 389 (600)
T ss_pred c
Confidence 4
No 7
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.88 E-value=3.5e-22 Score=194.02 Aligned_cols=159 Identities=27% Similarity=0.416 Sum_probs=132.7
Q ss_pred CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe---------cHHHHHHHHHH
Q 021032 25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG---------NYHSVQDALFH 95 (318)
Q Consensus 25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G---------~~~~V~~A~~~ 95 (318)
+...++|||++.+++|.||||+|..||+||.+|.++|+|.. ..+. ..||+|+|+| ..+++.+|..+
T Consensus 40 ~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~--~~~~---c~eRIiti~g~~~~~~~~~~~~al~ka~~~ 114 (485)
T KOG2190|consen 40 DETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNE--SLPG---CPERIITITGNRVELNLSPATDALFKAFDM 114 (485)
T ss_pred CCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeec--CCCC---CCcceEEEecccccccCCchHHHHHHHHHH
Confidence 45566899999999999999999999999999999999953 2444 4899999999 99999999999
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCC
Q 021032 96 ITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPM 175 (318)
Q Consensus 96 I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 175 (318)
|...+.+..... ..
T Consensus 115 iv~~~~~d~~~~-----------------------~d------------------------------------------- 128 (485)
T KOG2190|consen 115 IVFKLEEDDEAA-----------------------ED------------------------------------------- 128 (485)
T ss_pred Hhhccccccccc-----------------------cc-------------------------------------------
Confidence 988776431000 00
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccc
Q 021032 176 VPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLY 255 (318)
Q Consensus 176 ~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~ 255 (318)
. +.+. .....+.+|+||.+.
T Consensus 129 -----------~-------------------------------~~~~------------------~~~~v~~RLlVp~sq 148 (485)
T KOG2190|consen 129 -----------N-------------------------------GEDA------------------SGPEVTCRLLVPSSQ 148 (485)
T ss_pred -----------C-------------------------------Cccc------------------cCCceEEEEEechhh
Confidence 0 0000 011479999999999
Q ss_pred cccccccccchHHHHHHHhCCEEEEcCC-CCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032 256 MAHVYGENNSNLSHIRQISGANVVVNDP-KPGATEGVVMVSGTSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 256 vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~-~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~ 314 (318)
+|+||||+|+.||+||+.|||+|+|..+ .+.++||.|+|+|.+++|.+|...|..+|.+
T Consensus 149 ~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 149 VGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGEPDAVKKALVQISSRLLE 208 (485)
T ss_pred eeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCchHHHHHHHHHHHHHHHh
Confidence 9999999999999999999999999876 7889999999999999999999999999987
No 8
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.83 E-value=1e-20 Score=174.70 Aligned_cols=152 Identities=18% Similarity=0.295 Sum_probs=131.4
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCC
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFP 106 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~ 106 (318)
...+|+|||...+|.||||.|++||.|-..|-|+|+|-.++. .+..|+.++|.|.+|...+|+.+|++++...-.+
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~ 273 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN----AGAAEKIITVHSTPEGTSKACKMILEIMQKEAVD 273 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc----CCcccCceEEecCccchHHHHHHHHHHHHHhhhc
Confidence 478999999999999999999999999999999999987644 3578999999999999999999999999876221
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCC
Q 021032 107 MKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFP 186 (318)
Q Consensus 107 ~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~ 186 (318)
++
T Consensus 274 ~k------------------------------------------------------------------------------ 275 (584)
T KOG2193|consen 274 DK------------------------------------------------------------------------------ 275 (584)
T ss_pred cc------------------------------------------------------------------------------
Confidence 10
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccch
Q 021032 187 YGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSN 266 (318)
Q Consensus 187 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~ 266 (318)
....+.+++.-.+.+||++|||.|++
T Consensus 276 ------------------------------------------------------~~~e~pLk~lAHN~lvGRLIGKeGrn 301 (584)
T KOG2193|consen 276 ------------------------------------------------------VAEEIPLKILAHNNLVGRLIGKEGRN 301 (584)
T ss_pred ------------------------------------------------------hhhhcchhhhhhcchhhhhhhhcccc
Confidence 01234577778899999999999999
Q ss_pred HHHHHHHhCCEEEEcCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032 267 LSHIRQISGANVVVNDPKP---GATEGVVMVSGTSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 267 Ik~Ir~~SGA~I~i~~~~~---~~~er~v~I~Gt~~~v~~A~~lI~~~i~~ 314 (318)
||+|.+.||.+|.|+.-.+ ...||+|+++|+-|+|..|..+|..+|++
T Consensus 302 lKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre 352 (584)
T KOG2193|consen 302 LKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRE 352 (584)
T ss_pred HHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHH
Confidence 9999999999999987532 45799999999999999999999998864
No 9
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.80 E-value=4.1e-19 Score=155.62 Aligned_cols=148 Identities=22% Similarity=0.378 Sum_probs=129.8
Q ss_pred CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032 25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETI 104 (318)
Q Consensus 25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~ 104 (318)
...+++||||.++.+|.||||||++||.|+.+.+|.|+|... +..+|+++|+.+.+.|-+-++.|.-.|++..
T Consensus 45 ~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds-------~~peri~tisad~~ti~~ilk~iip~lee~f 117 (390)
T KOG2192|consen 45 RSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS-------SGPERILTISADIETIGEILKKIIPTLEEGF 117 (390)
T ss_pred hcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC-------CCCceeEEEeccHHHHHHHHHHHhhhhhhCC
Confidence 457999999999999999999999999999999999999643 2569999999999999999888888887751
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCC
Q 021032 105 FPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIP 184 (318)
Q Consensus 105 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 184 (318)
.
T Consensus 118 ~------------------------------------------------------------------------------- 118 (390)
T KOG2192|consen 118 Q------------------------------------------------------------------------------- 118 (390)
T ss_pred C-------------------------------------------------------------------------------
Confidence 1
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEeccccccccccccc
Q 021032 185 FPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENN 264 (318)
Q Consensus 185 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G 264 (318)
......++++|..+++|.|||++|
T Consensus 119 --------------------------------------------------------~~~pce~rllihqs~ag~iigrng 142 (390)
T KOG2192|consen 119 --------------------------------------------------------LPSPCELRLLIHQSLAGGIIGRNG 142 (390)
T ss_pred --------------------------------------------------------CCCchhhhhhhhhhhccceecccc
Confidence 000135788999999999999999
Q ss_pred chHHHHHHHhCCEEEEc-CCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032 265 SNLSHIRQISGANVVVN-DPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 265 ~~Ik~Ir~~SGA~I~i~-~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~ 314 (318)
++||+||+.+.|+++|- +..+.+++|+|.|.|.+..|..+...|.+.|++
T Consensus 143 skikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e 193 (390)
T KOG2192|consen 143 SKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISE 193 (390)
T ss_pred hhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhc
Confidence 99999999999999986 568899999999999999999999999888875
No 10
>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=99.75 E-value=1.3e-17 Score=142.55 Aligned_cols=61 Identities=21% Similarity=0.311 Sum_probs=54.4
Q ss_pred EEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEE---EecHHHHHHHHHHHHHHHHh
Q 021032 32 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQV---IGNYHSVQDALFHITSRLRE 102 (318)
Q Consensus 32 llVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I---~G~~~~V~~A~~~I~~~l~e 102 (318)
|-||.+.+|.|||+||++||+|+++|||+|+|.. .+..|.| +++++++.+|...|..+.+.
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 5689999999999999999999999999999953 2467888 89999999999999987765
No 11
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.71 E-value=1.8e-16 Score=142.83 Aligned_cols=203 Identities=20% Similarity=0.296 Sum_probs=143.1
Q ss_pred HHHHHHHHHHHHHhhccC----------------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCC
Q 021032 6 AQDAVMRVHSRIAEIGFE----------------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA 69 (318)
Q Consensus 6 a~~a~~~v~~~i~~~~~e----------------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~ 69 (318)
-.++|+-+|+.|.++..| .+..-.+|++||++-+|.||||||.+||.|+|++||.|+|++ ..
T Consensus 94 t~eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisP--qk 171 (402)
T KOG2191|consen 94 TVEALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISP--QK 171 (402)
T ss_pred cHHHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecc--cC
Confidence 468888888888876433 122356999999999999999999999999999999999985 23
Q ss_pred CCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 70 PRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPF 149 (318)
Q Consensus 70 p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~ 149 (318)
|..-+..||+|++.|++++..+|+.+|+++|.|+.. - .. + .+-+| +....|+.++
T Consensus 172 pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq--s----~s-c-ln~sy-----------------a~vsGpvaNs 226 (402)
T KOG2191|consen 172 PTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ--S----GS-C-LNISY-----------------ANVSGPVANS 226 (402)
T ss_pred CCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc--c----cc-e-eccch-----------------hcccCccccc
Confidence 455567899999999999999999999999999721 0 00 0 00000 0000010000
Q ss_pred CCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021032 150 HSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPR 229 (318)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~ 229 (318)
.+ .| .++++..
T Consensus 227 nP-----------------------------------tG---------------------------spya~~~------- 237 (402)
T KOG2191|consen 227 NP-----------------------------------TG---------------------------SPYAYQA------- 237 (402)
T ss_pred CC-----------------------------------CC---------------------------CCCCCCC-------
Confidence 00 00 0000000
Q ss_pred CCCCCCCCccccCcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCC---CCCCCeEEEEEcCHHHHHHHHH
Q 021032 230 NRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPK---PGATEGVVMVSGTSDQMRAAQS 306 (318)
Q Consensus 230 ~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~---~~~~er~v~I~Gt~~~v~~A~~ 306 (318)
.......+....++...+|..-|.+|.++..|...+|+.|.+.... .+...+ ..+.|.+-++..|..
T Consensus 238 ---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g 307 (402)
T KOG2191|consen 238 ---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEG 307 (402)
T ss_pred ---------ccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhhhhhh
Confidence 0011234456678889999999999999999999999999997653 245566 789999999999999
Q ss_pred HHHHHHHc
Q 021032 307 LIHAFILC 314 (318)
Q Consensus 307 lI~~~i~~ 314 (318)
+|...+..
T Consensus 308 ~L~~~~~~ 315 (402)
T KOG2191|consen 308 VLAAKVAS 315 (402)
T ss_pred HHHHhhcc
Confidence 99887754
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.71 E-value=1.7e-16 Score=136.51 Aligned_cols=65 Identities=18% Similarity=0.244 Sum_probs=58.2
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEE----ecHHHHHHHHHHHHHHHHh
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVI----GNYHSVQDALFHITSRLRE 102 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~----G~~~~V~~A~~~I~~~l~e 102 (318)
+...|.||.+.+|.|||++|++||.|+++|||+|+|.. .+..|.|. ++++++.+|...|..+++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~----------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS----------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC----------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 46789999999999999999999999999999999953 24788885 8999999999999988875
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=99.59 E-value=2.7e-15 Score=107.68 Aligned_cols=64 Identities=30% Similarity=0.488 Sum_probs=59.5
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC-CCCCeEEEEEcCHHHHHHHHHHHH
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP-GATEGVVMVSGTSDQMRAAQSLIH 309 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~-~~~er~v~I~Gt~~~v~~A~~lI~ 309 (318)
+.++.||.+.+|+||||+|++|++|++.|||+|.+.+... +..+|.|+|+|++++++.|..||+
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 3689999999999999999999999999999999987654 788999999999999999999984
No 14
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.59 E-value=4.1e-15 Score=106.74 Aligned_cols=64 Identities=39% Similarity=0.597 Sum_probs=58.0
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 96 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I 96 (318)
++||+||.+.+|+||||+|++|++|+++|||+|++.+.+. ....+|+|+|.|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 4799999999999999999999999999999999975432 346799999999999999999987
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=99.45 E-value=1.3e-13 Score=97.17 Aligned_cols=60 Identities=23% Similarity=0.511 Sum_probs=55.4
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHH
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLI 308 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI 308 (318)
|.+|.||.+++|+|||++|++|++|++.|||+|.|++. + .+..|+|+|++++++.|+.+|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence 67899999999999999999999999999999999765 3 555999999999999999987
No 16
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.43 E-value=2.3e-13 Score=96.58 Aligned_cols=61 Identities=23% Similarity=0.425 Sum_probs=56.3
Q ss_pred EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 309 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~ 309 (318)
.++.||.+++|+|||++|++|++|++.|||+|.+.+.. ..++.|+|+|+++++..|+.+|+
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 57889999999999999999999999999999997654 67899999999999999999874
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=99.41 E-value=7.7e-13 Score=94.19 Aligned_cols=63 Identities=27% Similarity=0.545 Sum_probs=58.8
Q ss_pred EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 309 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~ 309 (318)
.++.||.+++|+|||++|++|++|++.|||+|.|.+..++..++.|+|.|+.+++..|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHhC
Confidence 578999999999999999999999999999999988766778999999999999999999873
No 18
>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=99.38 E-value=1.6e-12 Score=91.96 Aligned_cols=59 Identities=19% Similarity=0.385 Sum_probs=53.9
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHH
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIH 309 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~ 309 (318)
.+..+.||.+++|+||||+|++|++|++.|||+|.|++ ++.|.|+|+ +++++.|+.+|.
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED------DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC------CCEEEEEeCCHHHHHHHHHHhC
Confidence 35778899999999999999999999999999999964 468999998 999999999873
No 19
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.36 E-value=9.8e-13 Score=92.69 Aligned_cols=60 Identities=27% Similarity=0.433 Sum_probs=54.1
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 96 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I 96 (318)
|.+|+||.+++|+||||+|++|++|+++|||+|+|... +.+..|+|+|+.++|.+|+.+|
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 68999999999999999999999999999999999643 2345999999999999999876
No 20
>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=99.36 E-value=1.7e-12 Score=92.15 Aligned_cols=60 Identities=17% Similarity=0.300 Sum_probs=54.7
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 96 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I 96 (318)
.+|.||..++|.|||++|++|++|+++|||+|+|.+.+ +.++.|+|+|+.++|.+|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~-------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG-------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC-------CCCCEEEEEcCHHHHHHHHHHh
Confidence 67999999999999999999999999999999996432 4689999999999999999876
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.36 E-value=3.5e-12 Score=90.16 Aligned_cols=58 Identities=19% Similarity=0.331 Sum_probs=52.8
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEec-HHHHHHHHHHH
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGN-YHSVQDALFHI 96 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~-~~~V~~A~~~I 96 (318)
.+..|-||.+++|.||||||++||+|+++|||+|.|. .++.|.|.|+ .+++.+|..+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~-----------~~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIE-----------DDGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeC-----------CCCEEEEEeCCHHHHHHHHHHh
Confidence 5678999999999999999999999999999999994 2578999998 99999999876
No 22
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.29 E-value=1.3e-11 Score=87.71 Aligned_cols=63 Identities=32% Similarity=0.550 Sum_probs=56.0
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHH
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHI 96 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I 96 (318)
+.+|.||.+++|.|||++|++|++|+++|||+|.|..... .+.++.|.|.|..+++.+|...|
T Consensus 1 ~~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred CEEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence 3689999999999999999999999999999999965322 35789999999999999998876
No 23
>PF13014 KH_3: KH domain
Probab=99.17 E-value=5.2e-11 Score=78.13 Aligned_cols=43 Identities=30% Similarity=0.696 Sum_probs=37.8
Q ss_pred cceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032 38 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84 (318)
Q Consensus 38 ~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G 84 (318)
++|+||||+|++|++|+++|||+|+|.+ + .+..+.+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~---~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-E---NEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-c---cCCCCCceEEEEEC
Confidence 5899999999999999999999999976 2 34457899999997
No 24
>PF13014 KH_3: KH domain
Probab=99.13 E-value=9.4e-11 Score=76.87 Aligned_cols=42 Identities=29% Similarity=0.659 Sum_probs=38.8
Q ss_pred ccccccccccchHHHHHHHhCCEEEEcC-CCCCCCCeEEEEEc
Q 021032 255 YMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSG 296 (318)
Q Consensus 255 ~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~-~~~~~~er~v~I~G 296 (318)
++|+||||+|++|++|+++|||+|+|.+ ..++..+|.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5799999999999999999999999987 45678999999998
No 25
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.11 E-value=3.9e-11 Score=115.13 Aligned_cols=147 Identities=20% Similarity=0.325 Sum_probs=123.6
Q ss_pred CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
..+.+.++++|+...+-++|||+|++||.|++.++++|.+-.+ +.+ .++...+.|-+.++..|.+.++.++.+.
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DVG-----DERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cCC-----cccchhhccCCCCCChHHHHHHHHHhcC
Confidence 3467889999999999999999999999999999999999643 333 4677777779999999999999888764
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCC
Q 021032 104 IFPMKRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRI 183 (318)
Q Consensus 104 ~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~ 183 (318)
-
T Consensus 138 ~------------------------------------------------------------------------------- 138 (608)
T KOG2279|consen 138 T------------------------------------------------------------------------------- 138 (608)
T ss_pred C-------------------------------------------------------------------------------
Confidence 0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccc
Q 021032 184 PFPYGSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGEN 263 (318)
Q Consensus 184 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~ 263 (318)
.+..++.+|...+++|+|++
T Consensus 139 ------------------------------------------------------------pvk~~lsvpqr~~~~i~grg 158 (608)
T KOG2279|consen 139 ------------------------------------------------------------PVSEQLSVPQRSVGRIIGRG 158 (608)
T ss_pred ------------------------------------------------------------cccccccchhhhcccccccc
Confidence 12345558888999999999
Q ss_pred cchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032 264 NSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG 315 (318)
Q Consensus 264 G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~ 315 (318)
|.++.+|+..|+|+|.+...--.-..+.+.|.|...-++.|+.++.+.++..
T Consensus 159 get~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 159 GETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSED 210 (608)
T ss_pred hhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccch
Confidence 9999999999999999987644456788999999999999999999888763
No 26
>smart00322 KH K homology RNA-binding domain.
Probab=99.11 E-value=5.2e-10 Score=79.72 Aligned_cols=66 Identities=26% Similarity=0.458 Sum_probs=59.8
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHH
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFI 312 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i 312 (318)
.+.++.||.+++|.+||++|++|++|++.+|++|.+..... ....|+|.|+.++++.|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 57899999999999999999999999999999999964332 6788999999999999999998876
No 27
>smart00322 KH K homology RNA-binding domain.
Probab=99.05 E-value=1.2e-09 Score=77.75 Aligned_cols=67 Identities=22% Similarity=0.470 Sum_probs=59.4
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHH
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRL 100 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l 100 (318)
.++.++.||...+|.|||++|++|++|++.||++|.+.... .....|.|.|+.+++..|...|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 46789999999999999999999999999999999995321 25789999999999999999998765
No 28
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.93 E-value=1.3e-08 Score=86.94 Aligned_cols=67 Identities=16% Similarity=0.221 Sum_probs=55.7
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe-----cHHHHHHHHHHHHHHHH
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG-----NYHSVQDALFHITSRLR 101 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G-----~~~~V~~A~~~I~~~l~ 101 (318)
.....+.||...+|.|||+.|++-+.|.+.+++++.+.. .+..|.|.- ++-.+.+|...|..+-+
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~----------~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr 76 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS----------KTGSVTIRTTRKTEDPLALLKARDVVKAIGR 76 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC----------CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence 445779999999999999999999999999999999963 356677664 57788899988877666
Q ss_pred hh
Q 021032 102 ET 103 (318)
Q Consensus 102 e~ 103 (318)
.+
T Consensus 77 GF 78 (194)
T COG1094 77 GF 78 (194)
T ss_pred CC
Confidence 64
No 29
>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=98.67 E-value=1e-07 Score=76.47 Aligned_cols=67 Identities=21% Similarity=0.352 Sum_probs=51.7
Q ss_pred ccceeeeCCCCchHHHHHHHhCCeEEEecCCCC-----------CCCCC-CCCceEEEEecH---HHHHHHHHHHHHHHH
Q 021032 37 QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA-----------PRCGS-PHDEIVQVIGNY---HSVQDALFHITSRLR 101 (318)
Q Consensus 37 ~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~-----------p~~~~-~~er~V~I~G~~---~~V~~A~~~I~~~l~ 101 (318)
+++|.|||.+|++||+|+++|||+|.|...... |.+.. +..-.|.|++.. +++.+|+..|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 568999999999999999999999999754221 11111 223568999965 899999999998887
Q ss_pred hh
Q 021032 102 ET 103 (318)
Q Consensus 102 e~ 103 (318)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
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=98.59 E-value=1.3e-07 Score=75.85 Aligned_cols=61 Identities=11% Similarity=0.244 Sum_probs=51.3
Q ss_pred cccccccccccchHHHHHHHhCCEEEEcCCCC-----------------CCCCeEEEEEcC---HHHHHHHHHHHHHHHH
Q 021032 254 LYMAHVYGENNSNLSHIRQISGANVVVNDPKP-----------------GATEGVVMVSGT---SDQMRAAQSLIHAFIL 313 (318)
Q Consensus 254 ~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~-----------------~~~er~v~I~Gt---~~~v~~A~~lI~~~i~ 313 (318)
+++|.|||.+|++||+|+++|||+|.|..... ....-.|.|++. .+++++|..+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 78999999999999999999999999976411 112367999995 5999999999999887
Q ss_pred c
Q 021032 314 C 314 (318)
Q Consensus 314 ~ 314 (318)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 5
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=98.57 E-value=7.8e-08 Score=82.24 Aligned_cols=60 Identities=17% Similarity=0.266 Sum_probs=54.0
Q ss_pred EEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEE---EcCHHHHHHHHHHHHHHHH
Q 021032 249 VVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMV---SGTSDQMRAAQSLIHAFIL 313 (318)
Q Consensus 249 v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I---~Gt~~~v~~A~~lI~~~i~ 313 (318)
+.||.+.+|.|||++|++|+.|++.|||+|+|+. ++..|.| +++++++.+|+.+|..+..
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~-----~~g~V~I~~~t~d~~~i~kA~~~I~~i~~ 64 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS-----ETGEVKIEEEDEDPLAVMKAREVVKAIGR 64 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc-----CCceEEEecCCCCHHHHHHHHHHHHHHHc
Confidence 5699999999999999999999999999999974 2367888 7899999999999998655
No 32
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.55 E-value=1.7e-07 Score=80.68 Aligned_cols=64 Identities=16% Similarity=0.245 Sum_probs=57.7
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEE----cCHHHHHHHHHHHHHHHH
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVS----GTSDQMRAAQSLIHAFIL 313 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~----Gt~~~v~~A~~lI~~~i~ 313 (318)
....+.||.+.+|.|||++|.+|+.|++.|||+|+|.+ +++.|.|. ++++++++|+.+|.+++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~-----~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS-----ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC-----CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 46789999999999999999999999999999999974 24788895 899999999999998765
No 33
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.22 E-value=4.9e-06 Score=86.07 Aligned_cols=139 Identities=16% Similarity=0.250 Sum_probs=111.8
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhhcCCC
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRETIFPM 107 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~~~~~ 107 (318)
+.+.+-+.......++||+|.+|.+|++++.+.|.+.. .++.+..|.++|...++.+|...|.....+.+.+
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~-------~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~- 418 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK-------QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS- 418 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc-------ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc-
Confidence 77888899999999999999999999999999999953 2467899999999999999999999888775110
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCCCCCCCCC
Q 021032 108 KRPGPNNGHSYLPPFPEMPPPPFRPRHNPASPGSYPSPVGPFHSMDRGMGPSQPFDHQAAFSHGMDPMVPPNSDRIPFPY 187 (318)
Q Consensus 108 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~g~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 187 (318)
T Consensus 419 -------------------------------------------------------------------------------- 418 (753)
T KOG2208|consen 419 -------------------------------------------------------------------------------- 418 (753)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccCcceEEEEEecccccccccccccchH
Q 021032 188 GSERPGHGPTFDRPPSPRSWTPQGVGGGDPRGFDASSGFTPRNRPVESGNHAAILTSTTIEVVIPQLYMAHVYGENNSNL 267 (318)
Q Consensus 188 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~t~~v~IP~~~vG~IIGk~G~~I 267 (318)
.....+.||...+.+|||.+|..|
T Consensus 419 --------------------------------------------------------~~~~~~~iP~k~~~~iig~~g~~i 442 (753)
T KOG2208|consen 419 --------------------------------------------------------IVKEEVQIPTKSHKRIIGTKGALI 442 (753)
T ss_pred --------------------------------------------------------cccceeecCccchhhhhccccccH
Confidence 123567799999999999999999
Q ss_pred HHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHH
Q 021032 268 SHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAF 311 (318)
Q Consensus 268 k~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~ 311 (318)
.+|...+|+ +.+......+....+++.|.-.-+..++.++..+
T Consensus 443 ~~I~~k~~~-v~i~f~~~~~~~~~~~~~~~~~dv~~~~~~~~~~ 485 (753)
T KOG2208|consen 443 NYIMGKHGG-VHIKFQNNNNSSDMVTIRGISKDVEKSVSLLKAL 485 (753)
T ss_pred HHHHhhcCc-EEEecCCCCcccccceEeccccccchhHHHHHhh
Confidence 999999995 5555455555666677888766666555554443
No 34
>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=98.22 E-value=6.3e-06 Score=83.88 Aligned_cols=87 Identities=22% Similarity=0.272 Sum_probs=73.3
Q ss_pred hHHHHHHHHHHHHHhhccCC-----CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032 5 PAQDAVMRVHSRIAEIGFEP-----GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI 79 (318)
Q Consensus 5 ~a~~a~~~v~~~i~~~~~e~-----~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~ 79 (318)
-|.++..+|++.+.+...++ ..+....|-||.+.+|.|||.||.+||+|+++|||+|.|. .+..
T Consensus 550 ~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-----------d~G~ 618 (719)
T TIGR02696 550 QARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-----------DDGT 618 (719)
T ss_pred HHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-----------cCcE
Confidence 46788888888777765433 3467899999999999999999999999999999999994 3688
Q ss_pred EEEEe-cHHHHHHHHHHHHHHHHh
Q 021032 80 VQVIG-NYHSVQDALFHITSRLRE 102 (318)
Q Consensus 80 V~I~G-~~~~V~~A~~~I~~~l~e 102 (318)
|.|.+ +.+.+.+|+.+|..++..
T Consensus 619 V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 619 VYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEEEeCCHHHHHHHHHHHHHhhCc
Confidence 99888 578999999999887774
No 35
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.17 E-value=4.9e-06 Score=68.63 Aligned_cols=62 Identities=15% Similarity=0.249 Sum_probs=46.1
Q ss_pred CChHHHHHHHHHHHHHhhccCC--CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032 3 HSPAQDAVMRVHSRIAEIGFEP--GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF 64 (318)
Q Consensus 3 ~s~a~~a~~~v~~~i~~~~~e~--~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~ 64 (318)
++..+=....+|+.+-....-. .+.-.+.++|+...+|..||++|++|+.|++..|-+|.|.
T Consensus 5 l~~~~~~~i~~fe~~t~~~~~dc~~d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv 68 (140)
T PRK08406 5 LTTEEIRYIALFESITGATVKDCIIDDDRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV 68 (140)
T ss_pred ECHHHHHHHHHHHHHhCCCceEEEEeCCEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE
Confidence 4445555667777765442100 1114588999999999999999999999999999999986
No 36
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.14 E-value=3.4e-06 Score=76.45 Aligned_cols=65 Identities=26% Similarity=0.360 Sum_probs=56.8
Q ss_pred CeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHH
Q 021032 26 QAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITS 98 (318)
Q Consensus 26 ~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~ 98 (318)
+.++..+-||..+++.|.|++|.+||.||.+|...|+-.... .|-+..++|..+.|+.|..+|-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~--------eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG--------EEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC--------CCCcceeccCchhHHHHhhcCcc
Confidence 678899999999999999999999999999999999976542 35678899999999999888743
No 37
>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=98.05 E-value=1.3e-05 Score=82.50 Aligned_cols=86 Identities=20% Similarity=0.363 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032 6 AQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI 79 (318)
Q Consensus 6 a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~ 79 (318)
|.++..+|++.+.+...+ +-.+....+-||...+|.|||+||++||+|+++|||+|.|. .+..
T Consensus 523 a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~-----------ddG~ 591 (684)
T TIGR03591 523 AKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIE-----------DDGT 591 (684)
T ss_pred HHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEe-----------cCeE
Confidence 556677777766665432 34577889999999999999999999999999999999994 3567
Q ss_pred EEEEe-cHHHHHHHHHHHHHHHHh
Q 021032 80 VQVIG-NYHSVQDALFHITSRLRE 102 (318)
Q Consensus 80 V~I~G-~~~~V~~A~~~I~~~l~e 102 (318)
|.|.+ ..+.+.+|...|..+..+
T Consensus 592 V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 592 VKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EEEEECcHHHHHHHHHHHHhhhcc
Confidence 77776 567888998888777543
No 38
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.01 E-value=3.4e-05 Score=74.93 Aligned_cols=74 Identities=22% Similarity=0.395 Sum_probs=62.1
Q ss_pred CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
+..+...+-+|...++.|+|++|.+|.+|+.-++|+|.+... .. ...++...|.|...-++.|..++.+++.+.
T Consensus 137 ~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr---~g~~~~~~i~~qqk~~~~a~~~~~~~~~ed 210 (608)
T KOG2279|consen 137 NTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GR---LGLSRLIKISGQQKEVAAAKHLILEKVSED 210 (608)
T ss_pred CCcccccccchhhhcccccccchhhhcchhcccccccccccc--cc---cccccceecccccchHHHHHhhhhccccch
Confidence 466778888999999999999999999999999999999543 21 145788999998888888988888887664
No 39
>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=97.92 E-value=2.3e-05 Score=79.89 Aligned_cols=64 Identities=25% Similarity=0.430 Sum_probs=58.1
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHH
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFIL 313 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~ 313 (318)
.....+.||.+.+|.|||.||.+||.|.++|||+|+|.+ +..|.|.+ +.+++++|+.+|..++.
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 356788899999999999999999999999999999953 67899999 67999999999999877
No 40
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.76 E-value=9.7e-05 Score=60.86 Aligned_cols=62 Identities=16% Similarity=0.295 Sum_probs=46.2
Q ss_pred CChHHHHHHHHHHHHHhhcc-C--CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032 3 HSPAQDAVMRVHSRIAEIGF-E--PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF 64 (318)
Q Consensus 3 ~s~a~~a~~~v~~~i~~~~~-e--~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~ 64 (318)
+++.+=..+.+|+.+..... + -++..-+=++|....+|..||++|++|+.|+|..|-+|.|.
T Consensus 5 l~~e~~~~i~lfe~~t~~~~~dc~~d~~~riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 5 LSTEAIKYIALFEDMTGATVVDCLIDDRNRVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred ECHHHHHHHHHHHHHhCCceEEEEecCCcEEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 45555666778877765421 0 01111677889999999999999999999999999999885
No 41
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.75 E-value=9.8e-05 Score=70.95 Aligned_cols=76 Identities=14% Similarity=0.247 Sum_probs=57.1
Q ss_pred eeEEEEEEec------ccceeeeCCCCchHHHHHHHhCCeEEEecCCC----------CCCCCCCC-CceEEEEecH-HH
Q 021032 27 AVVARLLVHS------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQ----------APRCGSPH-DEIVQVIGNY-HS 88 (318)
Q Consensus 27 ~~~~rllVp~------~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~----------~p~~~~~~-er~V~I~G~~-~~ 88 (318)
.++-||.||. +++|+|||-.|.|.|+|+++|||+|.|..+.. +..-..+. +--+.|+++. |.
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 6788999985 46999999999999999999999999975211 11111122 2347888865 68
Q ss_pred HHHHHHHHHHHHHh
Q 021032 89 VQDALFHITSRLRE 102 (318)
Q Consensus 89 V~~A~~~I~~~l~e 102 (318)
|.+|+..|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 88999988888865
No 42
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.73 E-value=0.00015 Score=75.25 Aligned_cols=70 Identities=20% Similarity=0.237 Sum_probs=61.1
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG 315 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~ 315 (318)
..-..+.|-..+...|+||+|.+|.+|++++.+.|.+.. .++++..+.++|....++.|...++..+.+-
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~--~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei 415 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPK--QGSNNKKVVITGVSANDEKAVEDVEKIIAEI 415 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceeccc--ccCCCCCeEEeccccchhHHHHHHHHHHHhh
Confidence 356777888999999999999999999999999999965 4567888999999999999999988877653
No 43
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.71 E-value=7.3e-05 Score=77.91 Aligned_cols=87 Identities=17% Similarity=0.270 Sum_probs=71.6
Q ss_pred hHHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCe-EEEecCCCCCCCCCCCC
Q 021032 5 PAQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGAS-IRVFPKDQAPRCGSPHD 77 (318)
Q Consensus 5 ~a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~-I~i~~~~~~p~~~~~~e 77 (318)
-|.++..+|++.+.+...+ +..+....|-||.+++|.|||.||.+||+|+++||++ |.|. .+
T Consensus 656 ~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------dd 724 (891)
T PLN00207 656 QAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DD 724 (891)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CC
Confidence 4677778888777665332 3567889999999999999999999999999999999 9983 36
Q ss_pred ceEEEEe-cHHHHHHHHHHHHHHHHh
Q 021032 78 EIVQVIG-NYHSVQDALFHITSRLRE 102 (318)
Q Consensus 78 r~V~I~G-~~~~V~~A~~~I~~~l~e 102 (318)
-.|.|.+ +.+.+.+|+..|..+..+
T Consensus 725 g~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 725 GTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 7788888 678999999998877754
No 44
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.69 E-value=0.00028 Score=63.15 Aligned_cols=81 Identities=15% Similarity=0.292 Sum_probs=54.1
Q ss_pred CeeEEEEEEecc------cceeeeCCCCchHHHHHHHhCCeEEEecCCCC------------CCCCCCCCc---eEEEEe
Q 021032 26 QAVVARLLVHSQ------QIGCLLGRGGHIVSEMRRATGASIRVFPKDQA------------PRCGSPHDE---IVQVIG 84 (318)
Q Consensus 26 ~~~~~rllVp~~------~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~------------p~~~~~~er---~V~I~G 84 (318)
-.++.||+||-. +||.|+|..|.++|+|+++|||+|.|..+.++ |.|+.-.+. .|+...
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 357899999965 69999999999999999999999999754332 344433332 456666
Q ss_pred cHHHHHHHHHHHHHHHHhhcCC
Q 021032 85 NYHSVQDALFHITSRLRETIFP 106 (318)
Q Consensus 85 ~~~~V~~A~~~I~~~l~e~~~~ 106 (318)
++.-+..=+.+-.+.|++.|.|
T Consensus 170 p~~ea~~rl~~AleeI~klL~P 191 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLLVP 191 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhcCC
Confidence 6654443333333444444443
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.63 E-value=0.00016 Score=69.48 Aligned_cols=72 Identities=17% Similarity=0.328 Sum_probs=57.0
Q ss_pred ceEEEEEecc------cccccccccccchHHHHHHHhCCEEEEcCC---------------CCCCC-CeEEEEEc-CHHH
Q 021032 244 STTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVNDP---------------KPGAT-EGVVMVSG-TSDQ 300 (318)
Q Consensus 244 ~~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~---------------~~~~~-er~v~I~G-t~~~ 300 (318)
..+-+|.||. +|||.|||-.|.+.|+|.++|||+|.|-.. .+... +=-+.|++ |.|.
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 4566777775 699999999999999999999999999541 11222 23477888 6799
Q ss_pred HHHHHHHHHHHHHcC
Q 021032 301 MRAAQSLIHAFILCG 315 (318)
Q Consensus 301 v~~A~~lI~~~i~~~ 315 (318)
|++|..+|+.+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999864
No 46
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.62 E-value=0.0001 Score=75.97 Aligned_cols=65 Identities=18% Similarity=0.290 Sum_probs=56.8
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHc
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~ 314 (318)
.....+.||.+.+|.|||++|.+||+|.++|||+|.|.+ +..|.|.+ ..+.+++|+.+|..+...
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 456788999999999999999999999999999999953 57788887 578999999999887653
No 47
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.42 E-value=0.00041 Score=69.13 Aligned_cols=69 Identities=19% Similarity=0.381 Sum_probs=59.7
Q ss_pred cceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032 243 TSTTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 243 ~~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~ 316 (318)
...+..|.+|+ ++-|+||||.|.||+-+...||++|-|++.. ..|+|+| .|---+.|+..|..+|..|+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp-----~~v~ls~fdp~rreia~~~l~~li~dgr 272 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP-----EAVILSGFDPVRREIARMALEKLIQDGR 272 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC-----CeEEecCCchHHHHHHHHHHHHHHHcCC
Confidence 34667788998 7779999999999999999999999997533 3588999 78888999999999999875
No 48
>PRK00106 hypothetical protein; Provisional
Probab=97.41 E-value=0.00045 Score=68.77 Aligned_cols=69 Identities=22% Similarity=0.406 Sum_probs=60.0
Q ss_pred cceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032 243 TSTTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 243 ~~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~ 316 (318)
...+..|.+|+ ++-|+||||.|.||+-+...||++|-|++.. ..|+|+| .|---+-|+..|..+|..|+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~v~lS~fdpvRReiAr~~le~Li~dgr 293 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP-----EVVVLSGFDPIRREIARMTLESLIKDGR 293 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC-----CeEEEeCCChHHHHHHHHHHHHHHHcCC
Confidence 34667788998 7789999999999999999999999997533 3588999 89999999999999999886
No 49
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.40 E-value=0.00023 Score=65.49 Aligned_cols=71 Identities=23% Similarity=0.284 Sum_probs=58.9
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
....-++|+++..|+|||+.|.|-|+|+++|+++|.++... ...+.++.+.+..++|.+|...|...|.+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 35678899999999999999999999999999999996542 133455555568899999999999888776
No 50
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.40 E-value=0.00015 Score=68.66 Aligned_cols=69 Identities=20% Similarity=0.326 Sum_probs=57.3
Q ss_pred CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHH
Q 021032 25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 101 (318)
Q Consensus 25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~ 101 (318)
.....+.|-|-+..||.+||+||++||.||..|+++|+|... ..+-.|+|.|..+--.+|...|-...+
T Consensus 44 ~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 44 GGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 456788999999999999999999999999999999999743 457889999988866666666644443
No 51
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.38 E-value=0.00019 Score=67.96 Aligned_cols=68 Identities=15% Similarity=0.112 Sum_probs=57.4
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~ 314 (318)
...+-+.|-.++||.|||++|++|+.|+..+..+|+|.+.. .|-.|+|-|..+--.+|+..|...+..
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~---~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD---LEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC---ceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 34566778899999999999999999999999999997654 467899999998888888887766543
No 52
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.37 E-value=0.00029 Score=72.74 Aligned_cols=87 Identities=21% Similarity=0.324 Sum_probs=69.4
Q ss_pred hHHHHHHHHHHHHHhhccCC------CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc
Q 021032 5 PAQDAVMRVHSRIAEIGFEP------GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE 78 (318)
Q Consensus 5 ~a~~a~~~v~~~i~~~~~e~------~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er 78 (318)
-|.++..+|++.+.+...++ ..+....+-|+...++.+||.||.+||+|+++||++|.+. .+.
T Consensus 525 ~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G 593 (693)
T PRK11824 525 QAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDG 593 (693)
T ss_pred HHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCc
Confidence 46778888888887765432 3455567778999999999999999999999999998882 367
Q ss_pred eEEEEe-cHHHHHHHHHHHHHHHHh
Q 021032 79 IVQVIG-NYHSVQDALFHITSRLRE 102 (318)
Q Consensus 79 ~V~I~G-~~~~V~~A~~~I~~~l~e 102 (318)
.|.|.+ ..+.+.+|...|..+..+
T Consensus 594 ~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 594 TVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred eEEEEcccHHHHHHHHHHHHHhccc
Confidence 788888 678888999988776644
No 53
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.36 E-value=0.00064 Score=68.33 Aligned_cols=87 Identities=22% Similarity=0.309 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032 6 AQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI 79 (318)
Q Consensus 6 a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~ 79 (318)
|-+|-++++..+.+.-.+ +-.+-...+-|+...++-+||+||.+|++|.++|||+|+|. .+..
T Consensus 524 Ak~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGt 592 (692)
T COG1185 524 AKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGT 592 (692)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCc
Confidence 556777777776665332 23456678889999999999999999999999999999993 3678
Q ss_pred EEEEecH-HHHHHHHHHHHHHHHhh
Q 021032 80 VQVIGNY-HSVQDALFHITSRLRET 103 (318)
Q Consensus 80 V~I~G~~-~~V~~A~~~I~~~l~e~ 103 (318)
|.|.+.. +.+.+|+..|..+.++.
T Consensus 593 v~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 593 VKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred EEEEecchHHHHHHHHHHHHHHhhc
Confidence 9999876 78889999999988775
No 54
>PRK12704 phosphodiesterase; Provisional
Probab=97.27 E-value=0.00072 Score=67.53 Aligned_cols=69 Identities=17% Similarity=0.370 Sum_probs=57.7
Q ss_pred cceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032 243 TSTTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 243 ~~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~ 316 (318)
...+..|.+|+ ++-|+||||.|.||+-+...||++|-|++. -..|+||| .|-.-+.|+..|..++..|+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt-----p~~v~ls~~~~~rre~a~~~l~~l~~dg~ 278 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT-----PEAVILSGFDPIRREIARLALEKLVQDGR 278 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC-----CCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence 34566778998 778999999999999999999999999753 34588999 67777789999988888775
No 55
>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=97.24 E-value=0.00054 Score=48.21 Aligned_cols=37 Identities=30% Similarity=0.514 Sum_probs=34.6
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEE
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV 63 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i 63 (318)
.....+.|+..++|..|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4789999999999999999999999999999988876
No 56
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.18 E-value=0.001 Score=57.14 Aligned_cols=54 Identities=24% Similarity=0.405 Sum_probs=49.1
Q ss_pred cceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 38 QIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 38 ~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
..|.|||++|.+-+-|++-|||.|.|. +..|.|-|.+++|+.|...|..++...
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~------------g~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVY------------GKTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEe------------CcEEEEecChhhhHHHHHHHHHHHcCC
Confidence 469999999999999999999999995 567999999999999999998888664
No 57
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.17 E-value=0.001 Score=59.76 Aligned_cols=65 Identities=18% Similarity=0.308 Sum_probs=55.9
Q ss_pred EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcC-HHHHHHHHHHHHHHHHcCcC
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGT-SDQMRAAQSLIHAFILCGVT 317 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt-~~~v~~A~~lI~~~i~~~~~ 317 (318)
..+.||.++++++||++|.+|+.|.+.++++|.|. .+..|.|+++ .+.+.+|+.+|+.+-++-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG------QNGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 56779999999999999999999999999999994 3577899995 56999999999987665443
No 58
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=97.13 E-value=0.00063 Score=47.83 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=33.9
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEE
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV 280 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i 280 (318)
....+.|+.+.+|.+|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999999988876
No 59
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.08 E-value=0.00065 Score=71.00 Aligned_cols=65 Identities=9% Similarity=0.245 Sum_probs=57.6
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCE-EEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHc
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGAN-VVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~-I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~ 314 (318)
.....+.||.+.+|.|||.||.+|+.|.++||+. |++. ++..|.|.+ +.+.+++|+.+|.+++..
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 4567889999999999999999999999999999 9995 367889999 689999999999988653
No 60
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.97 E-value=0.0012 Score=66.33 Aligned_cols=65 Identities=15% Similarity=0.269 Sum_probs=57.6
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCH-HHHHHHHHHHHHHHHc
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTS-DQMRAAQSLIHAFILC 314 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~-~~v~~A~~lI~~~i~~ 314 (318)
....++.|+.+.++-|||++|.+|++|.++|||+|+|. ++.+|.|.++. +.+..|+..|.+++.+
T Consensus 551 Pri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie------ddGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 551 PRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE------DDGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred CceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec------CCCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 45677889999999999999999999999999999994 45679999965 8999999999998754
No 61
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.80 E-value=0.002 Score=55.74 Aligned_cols=37 Identities=19% Similarity=0.325 Sum_probs=34.8
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
...+.||.+..+..|||+|.+++.+++.||-+|.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6888899999999999999999999999999999954
No 62
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.73 E-value=0.0037 Score=53.93 Aligned_cols=78 Identities=12% Similarity=0.201 Sum_probs=53.6
Q ss_pred CeeEEEEEEec------ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCC---------CCce---EEEEecHH
Q 021032 26 QAVVARLLVHS------QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSP---------HDEI---VQVIGNYH 87 (318)
Q Consensus 26 ~~~~~rllVp~------~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~---------~er~---V~I~G~~~ 87 (318)
..++-++.||- ++||+|||..|+|+|+|++.|+|+|.|-.+...-.|-.+ .+.+ +.+.-..+
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsed 225 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSED 225 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhh
Confidence 45677888874 679999999999999999999999999753222122111 1211 22233445
Q ss_pred HHHHHHHHHHHHHHhh
Q 021032 88 SVQDALFHITSRLRET 103 (318)
Q Consensus 88 ~V~~A~~~I~~~l~e~ 103 (318)
.+++++..+...++++
T Consensus 226 ki~~~ik~~~n~I~~a 241 (269)
T COG5176 226 KICRLIKSQLNAIREA 241 (269)
T ss_pred hHHHHHHHHHHHHHHH
Confidence 6777888888888886
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.72 E-value=0.0024 Score=58.95 Aligned_cols=71 Identities=10% Similarity=0.237 Sum_probs=57.9
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~ 316 (318)
.....+.++..+.|.|||++|.+.+.|+++|+++|.++.+. .....|+|+| ..++|.+|..-|.-+|.+.+
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~--~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN--TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC--CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 45567789999999999999999999999999999996554 3344455555 78999999999988887644
No 64
>PRK00468 hypothetical protein; Provisional
Probab=96.68 E-value=0.0019 Score=47.32 Aligned_cols=33 Identities=27% Similarity=0.529 Sum_probs=29.8
Q ss_pred CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032 24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA 56 (318)
Q Consensus 24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~ 56 (318)
.++.+.++|-|...-+|.||||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 456789999999999999999999999999854
No 65
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=96.65 E-value=0.0044 Score=45.32 Aligned_cols=33 Identities=21% Similarity=0.456 Sum_probs=29.9
Q ss_pred CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032 24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA 56 (318)
Q Consensus 24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~ 56 (318)
.+..+.++|-|....+|.+|||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 467889999999999999999999999999953
No 66
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.58 E-value=0.0027 Score=56.93 Aligned_cols=39 Identities=15% Similarity=0.472 Sum_probs=34.9
Q ss_pred cceEEEEEecc------cccccccccccchHHHHHHHhCCEEEEc
Q 021032 243 TSTTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVN 281 (318)
Q Consensus 243 ~~~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~ 281 (318)
...+.+|.||. ++||+|+|..|.++|+|+++|||+|.|-
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 35778888886 5999999999999999999999999994
No 67
>PRK12705 hypothetical protein; Provisional
Probab=96.47 E-value=0.004 Score=61.70 Aligned_cols=68 Identities=16% Similarity=0.326 Sum_probs=56.1
Q ss_pred ceEEEEEecc-cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032 244 STTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 244 ~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~ 316 (318)
..+..|.+|+ ++-|+||||.|.||+-+...||..|.|++.. ..|+|++ .|.--+.|...+..+|..|+
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp-----~~V~ls~fdp~rreia~~~l~~Li~dgr 266 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP-----EAVVISSFNPIRREIARLTLEKLLADGR 266 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc-----cchhhcccCccchHHHHHHHHHHHhcCC
Confidence 4566678887 6779999999999999999999999997533 3377888 67788888888888888775
No 68
>PRK01064 hypothetical protein; Provisional
Probab=96.45 E-value=0.0079 Score=44.40 Aligned_cols=33 Identities=21% Similarity=0.477 Sum_probs=30.0
Q ss_pred CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032 24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA 56 (318)
Q Consensus 24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~ 56 (318)
.+..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 467789999999999999999999999999864
No 69
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=96.44 E-value=0.00085 Score=70.34 Aligned_cols=73 Identities=21% Similarity=0.159 Sum_probs=62.6
Q ss_pred CcceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC-CCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHc
Q 021032 242 LTSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND-PKPGATEGVVMVSGTSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 242 ~~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~-~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~ 314 (318)
.......+.+|.....+|||++|++|+.+|.-+||.|.|.+ ..++..||.+.+.|+++.++.|..+|.-.|..
T Consensus 1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeec
Confidence 34455678899999999999999999999999999999987 34457899999999999999999988765543
No 70
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.41 E-value=0.0066 Score=54.55 Aligned_cols=63 Identities=17% Similarity=0.266 Sum_probs=51.5
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHH-HHHHHHHHHHHHHHhh
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH-SVQDALFHITSRLRET 103 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~-~V~~A~~~I~~~l~e~ 103 (318)
+.+-||...++.|||++|.+|+.|.++++++|.|- .+-.|.|.+... ++.+|...|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 45788999999999999999999999999999993 257788888654 7777777776655554
No 71
>PRK02821 hypothetical protein; Provisional
Probab=96.33 E-value=0.0077 Score=44.33 Aligned_cols=33 Identities=24% Similarity=0.538 Sum_probs=29.2
Q ss_pred CCCeeEEEEEEecccceeeeCCCCchHHHHHHH
Q 021032 24 PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRA 56 (318)
Q Consensus 24 ~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~ 56 (318)
.++.+.+.|-|...-+|.||||+|.+|+.||.-
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTV 59 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHH
Confidence 355688999999999999999999999999954
No 72
>PRK00468 hypothetical protein; Provisional
Probab=96.33 E-value=0.004 Score=45.62 Aligned_cols=31 Identities=23% Similarity=0.309 Sum_probs=28.5
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHh
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
...+++.+..+-+|+||||+|.+|+.||..-
T Consensus 29 ~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 29 SVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 4788999999999999999999999999874
No 73
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.24 E-value=0.43 Score=41.89 Aligned_cols=65 Identities=17% Similarity=0.237 Sum_probs=54.2
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
.+.+.++....-.|...+|..++.|-...||+|.+.. .+..|.|+|+...+..+...|.+.+...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~----------~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR----------SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec----------CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 3455556888899999999999999888899999964 4789999999999988888887777664
No 74
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.22 E-value=0.0043 Score=64.23 Aligned_cols=64 Identities=19% Similarity=0.319 Sum_probs=55.1
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHc
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILC 314 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~ 314 (318)
....+.||.+.++.+||.||.+|+.|.+++|+.|++. ++..|.|.+ ..+.+++|+.+|..++..
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 3456778999999999999999999999999998883 357789999 678999999999987753
No 75
>PRK02821 hypothetical protein; Provisional
Probab=96.18 E-value=0.0052 Score=45.21 Aligned_cols=33 Identities=21% Similarity=0.327 Sum_probs=29.5
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCC
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGA 276 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA 276 (318)
...+++.+..+-+|+||||+|.+|+.||..-.|
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 467899999999999999999999999998544
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.05 E-value=0.012 Score=50.91 Aligned_cols=39 Identities=21% Similarity=0.400 Sum_probs=32.7
Q ss_pred ceEEEEEecc------cccccccccccchHHHHHHHhCCEEEEcC
Q 021032 244 STTIEVVIPQ------LYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 244 ~~t~~v~IP~------~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
..+-.++||- ++||.|||..|.++|++++.|+|+|-|-.
T Consensus 147 k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG 191 (269)
T COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRG 191 (269)
T ss_pred cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEec
Confidence 3455566653 79999999999999999999999999954
No 77
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.03 E-value=0.017 Score=54.73 Aligned_cols=38 Identities=24% Similarity=0.408 Sum_probs=35.5
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
....+.||.+..+..|||+|.|++-.++.||.+|.|..
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 46889999999999999999999999999999999953
No 78
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.01 E-value=0.013 Score=55.80 Aligned_cols=38 Identities=16% Similarity=0.235 Sum_probs=35.2
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
....+.||.+..+..|||+|.|++-.++.||.+|+|..
T Consensus 308 ~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s 345 (374)
T PRK12328 308 KKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNE 345 (374)
T ss_pred cEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEE
Confidence 46788999999999999999999999999999999954
No 79
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.61 E-value=0.013 Score=42.82 Aligned_cols=32 Identities=25% Similarity=0.397 Sum_probs=28.8
Q ss_pred cceEEEEEecccccccccccccchHHHHHHHh
Q 021032 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
....+++.+..+-+|.||||+|.+|+.||..-
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 35779999999999999999999999999874
No 80
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.59 E-value=0.03 Score=53.40 Aligned_cols=38 Identities=16% Similarity=0.361 Sum_probs=35.4
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
....+.||.+..+..|||+|.|++--++.||.+|.|..
T Consensus 303 ~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 303 KAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred cEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 46889999999999999999999999999999999964
No 81
>PRK01064 hypothetical protein; Provisional
Probab=95.46 E-value=0.012 Score=43.46 Aligned_cols=32 Identities=13% Similarity=0.328 Sum_probs=28.7
Q ss_pred cceEEEEEecccccccccccccchHHHHHHHh
Q 021032 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
....+++.|..+-.|++|||+|.+|+.||...
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 35789999999999999999999999999964
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.37 E-value=0.042 Score=54.22 Aligned_cols=38 Identities=18% Similarity=0.375 Sum_probs=35.6
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
....+.||.+..+.-|||+|.|++..++.||.+|.|..
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47889999999999999999999999999999999964
No 83
>PRK12704 phosphodiesterase; Provisional
Probab=95.34 E-value=0.076 Score=53.22 Aligned_cols=49 Identities=20% Similarity=0.350 Sum_probs=39.9
Q ss_pred CeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032 26 QAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84 (318)
Q Consensus 26 ~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G 84 (318)
+..+--+-+|+ ..-|.||||.|.+||.++.-||++|-|. ++-.+|.|+|
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~ 257 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSG 257 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc----------CCCCeEEEec
Confidence 34555666787 6789999999999999999999999994 2456777888
No 84
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=95.32 E-value=0.014 Score=53.53 Aligned_cols=65 Identities=18% Similarity=0.306 Sum_probs=55.5
Q ss_pred cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHH
Q 021032 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHA 310 (318)
Q Consensus 243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~ 310 (318)
..++..+.||..+++.|.|++|.+||.||..|...|+-... ..|-++.++|.++.|..|++-|..
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 35788889999999999999999999999999988876422 245889999999999999987754
No 85
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=95.28 E-value=0.01 Score=51.01 Aligned_cols=64 Identities=19% Similarity=0.271 Sum_probs=54.5
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
.+++=.=-+..+|.|+||+|.+--.|++.|.++|.+. +..+.|-|..++++-|...||.++...
T Consensus 169 KtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 169 KTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred ccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccC
Confidence 3444444456799999999999999999999999984 567899999999999999999998774
No 86
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.26 E-value=0.086 Score=52.76 Aligned_cols=50 Identities=20% Similarity=0.347 Sum_probs=40.2
Q ss_pred CCeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032 25 GQAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84 (318)
Q Consensus 25 ~~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G 84 (318)
.+..+.-+-+|+ ..-|.||||.|.+||.++..||++|-|. ++-..|.|++
T Consensus 201 ~e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid----------dtp~~v~ls~ 251 (514)
T TIGR03319 201 AETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID----------DTPEAVILSG 251 (514)
T ss_pred hhheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc----------CCCCeEEecC
Confidence 345556677887 6789999999999999999999999994 2345677777
No 87
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.15 E-value=0.053 Score=52.57 Aligned_cols=38 Identities=16% Similarity=0.355 Sum_probs=35.1
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
....+.||.+..+..|||+|.|++--...||.+|.|..
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 35789999999999999999999999999999999964
No 88
>PRK00106 hypothetical protein; Provisional
Probab=95.12 E-value=0.12 Score=51.79 Aligned_cols=50 Identities=18% Similarity=0.359 Sum_probs=40.7
Q ss_pred CCeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEe
Q 021032 25 GQAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIG 84 (318)
Q Consensus 25 ~~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G 84 (318)
.+..+.-+-+|+ ..-|.||||.|.+|+.++.-||++|-|. ++-..|.|+|
T Consensus 222 ~e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~ 272 (535)
T PRK00106 222 TEQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSG 272 (535)
T ss_pred hhheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeC
Confidence 345556677887 5789999999999999999999999994 2446677887
No 89
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=94.78 E-value=0.026 Score=40.65 Aligned_cols=36 Identities=22% Similarity=0.480 Sum_probs=30.3
Q ss_pred EEEEEeccc-----ceeeeCCCCchHHHHHHHh-CCeEEEec
Q 021032 30 ARLLVHSQQ-----IGCLLGRGGHIVSEMRRAT-GASIRVFP 65 (318)
Q Consensus 30 ~rllVp~~~-----vG~IIGkgG~~Ik~I~e~t-Ga~I~i~~ 65 (318)
+++.|-... +|..||++|++||.|.++. |-+|+|..
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 567777777 9999999999999999999 99999964
No 90
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.32 E-value=0.11 Score=51.42 Aligned_cols=86 Identities=17% Similarity=0.265 Sum_probs=65.8
Q ss_pred HHHHHHHHHHHHHhhccC------CCCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCce
Q 021032 6 AQDAVMRVHSRIAEIGFE------PGQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEI 79 (318)
Q Consensus 6 a~~a~~~v~~~i~~~~~e------~~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~ 79 (318)
|.+|-++|++.+.+.-.+ ...++...|-|+.++.-.+||.+|...|+|+.+||+.-++ +|..
T Consensus 569 a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t 636 (760)
T KOG1067|consen 569 AREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGT 636 (760)
T ss_pred hhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCce
Confidence 455666666665544322 3568889999999999999999999999999999965555 3566
Q ss_pred EEEEe-cHHHHHHHHHHHHHHHHhh
Q 021032 80 VQVIG-NYHSVQDALFHITSRLRET 103 (318)
Q Consensus 80 V~I~G-~~~~V~~A~~~I~~~l~e~ 103 (318)
+.|-. +..+.++|...|..++...
T Consensus 637 ~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 637 FSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred EEEEecCHHHHHHHHHHHHHHhcCc
Confidence 77766 5677789999998887663
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=94.15 E-value=0.089 Score=36.79 Aligned_cols=35 Identities=14% Similarity=0.317 Sum_probs=28.4
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeE
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I 61 (318)
...+.+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45566666666799999999999999999988543
No 92
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=93.94 E-value=0.076 Score=43.78 Aligned_cols=38 Identities=16% Similarity=0.279 Sum_probs=34.4
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
...-+.|+...+|..||++|++|+.|++..|-+|+|-+
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 56778889999999999999999999999999999843
No 93
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=93.52 E-value=0.25 Score=48.98 Aligned_cols=65 Identities=20% Similarity=0.170 Sum_probs=55.5
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEc-CHHHHHHHHHHHHHHHHcCc
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSG-TSDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~G-t~~~v~~A~~lI~~~i~~~~ 316 (318)
....+.|+.+..-.+||.+|-+.|+|..+|||.-.+ +|.++.|.- ++.+.+.|+.+|..++..++
T Consensus 597 ~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v-------De~t~~i~A~~~~am~~Ak~~I~~i~~~~~ 662 (760)
T KOG1067|consen 597 VLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV-------DEGTFSIFAPTQAAMEEAKEFIDGIIKDDQ 662 (760)
T ss_pred eeeEEeecchhhheeecCccceeeeEeeeccceeee-------cCceEEEEecCHHHHHHHHHHHHHHhcCcc
Confidence 456778999999999999999999999999965555 466788887 78999999999999887643
No 94
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.51 E-value=0.033 Score=40.38 Aligned_cols=34 Identities=12% Similarity=0.291 Sum_probs=28.5
Q ss_pred CCeeEEEEEEecccceeeeCCCCchHHHHHHHhC
Q 021032 25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATG 58 (318)
Q Consensus 25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tG 58 (318)
.+...+.+-|.....|.||||.|.+++.||--.+
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4556788888999999999999999999985443
No 95
>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=93.48 E-value=0.038 Score=40.57 Aligned_cols=35 Identities=14% Similarity=0.351 Sum_probs=29.9
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEE
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIR 62 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~ 62 (318)
..+.+.+..++.|.+|||+|++|++|++..+-.+.
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 45788899999999999999999999987765553
No 96
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.87 E-value=0.066 Score=38.80 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=29.1
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCC
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGA 276 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA 276 (318)
...+.+.+..+..|.+|||.|.+++.||....+
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 457888899999999999999999999988754
No 97
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=92.16 E-value=0.28 Score=43.73 Aligned_cols=58 Identities=24% Similarity=0.390 Sum_probs=43.4
Q ss_pred EEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHH-HHHHHHHHHHH
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSD-QMRAAQSLIHA 310 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~-~v~~A~~lI~~ 310 (318)
.-+.|+...+-++|||+|+.++.|.+.++|+|.|. ....|-|.|..+ ....|...|..
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG------~NG~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG------QNGRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe------cCCEEEecCCCcchHHHHHHHHHH
Confidence 55779999999999999999999999999999994 334456666555 24444444443
No 98
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=92.04 E-value=0.1 Score=45.00 Aligned_cols=53 Identities=15% Similarity=0.340 Sum_probs=48.1
Q ss_pred cccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHH
Q 021032 254 LYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFIL 313 (318)
Q Consensus 254 ~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~ 313 (318)
..+|+|+||+|.+---|.+.|..+|.+. +..|.|-|+.+.++.|+..|..+|.
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVla-------d~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLA-------DSKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEec-------CceEEEeecchhhHHHHHhhHhhhc
Confidence 4689999999999999999999999995 3559999999999999999998875
No 99
>PRK12705 hypothetical protein; Provisional
Probab=92.00 E-value=0.37 Score=48.03 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=32.7
Q ss_pred CeeEEEEEEec-ccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032 26 QAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATGASIRVF 64 (318)
Q Consensus 26 ~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tGa~I~i~ 64 (318)
+..+--+-+|+ ..-|.||||.|.+|+.++..||+.|-|.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 34445566776 5789999999999999999999999995
No 100
>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=91.93 E-value=0.27 Score=34.28 Aligned_cols=34 Identities=15% Similarity=0.232 Sum_probs=27.2
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEE
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV 278 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I 278 (318)
....+.+.....|.+|||+|.+|+.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666665689999999999999999998544
No 101
>PRK13764 ATPase; Provisional
Probab=91.70 E-value=0.29 Score=49.83 Aligned_cols=44 Identities=27% Similarity=0.499 Sum_probs=38.1
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCC
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAP 70 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p 70 (318)
.-..-+.||...++.+|||+|.+|++|+++.|.+|.|-+.+..+
T Consensus 480 ~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 480 DNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 34567889999999999999999999999999999998765443
No 102
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=91.53 E-value=0.22 Score=36.47 Aligned_cols=33 Identities=15% Similarity=0.409 Sum_probs=26.1
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeE
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASI 61 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I 61 (318)
.+.+-|.....|.||||.|++++.||-=...-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 356667788999999999999999996555333
No 103
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=91.41 E-value=0.21 Score=35.90 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=27.9
Q ss_pred EEEEecccc-----cccccccccchHHHHHHHh-CCEEEEcC
Q 021032 247 IEVVIPQLY-----MAHVYGENNSNLSHIRQIS-GANVVVND 282 (318)
Q Consensus 247 ~~v~IP~~~-----vG~IIGk~G~~Ik~Ir~~S-GA~I~i~~ 282 (318)
..+.|-... +|..||++|.+|+.|.++. |-+|+|-+
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 444555555 8999999999999999999 99999854
No 104
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=91.20 E-value=0.21 Score=48.62 Aligned_cols=38 Identities=29% Similarity=0.450 Sum_probs=34.8
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
.+.+.||...++.+|||+|.+|++|+++.|.+|.|-+.
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 46688999999999999999999999999999999754
No 105
>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=91.13 E-value=0.27 Score=36.52 Aligned_cols=36 Identities=11% Similarity=0.293 Sum_probs=29.6
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEE
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRV 63 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i 63 (318)
-.+++.|....-|.||||+|+.|++|+++-.-...+
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 448899999999999999999999999875544433
No 106
>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=91.08 E-value=0.26 Score=40.65 Aligned_cols=37 Identities=14% Similarity=0.326 Sum_probs=33.2
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
..-+.|....+|..||++|++|+.|++..|-+|+|-+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 5667788899999999999999999999999999843
No 107
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.80 E-value=0.063 Score=57.03 Aligned_cols=69 Identities=20% Similarity=0.124 Sum_probs=57.4
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 102 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e 102 (318)
-++-+|......+||+||++|..+|+.|||-|.|-. .-|. .-.||.+.+.|.++.++-|...|.-.+.+
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielek--mq~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEK--MQPD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhh--cCCc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 467789899999999999999999999999999843 2221 13589999999999999999888766655
No 108
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=90.60 E-value=0.29 Score=41.41 Aligned_cols=34 Identities=35% Similarity=0.576 Sum_probs=30.3
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHHhCCeEEEe
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVF 64 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~ 64 (318)
+=++|-... |.-|||+|.+||.+++..|-+|.+.
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 456777777 9999999999999999999999996
No 109
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=90.56 E-value=0.19 Score=36.83 Aligned_cols=34 Identities=26% Similarity=0.307 Sum_probs=29.1
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEE
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANV 278 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I 278 (318)
....+.+-...-|.|||++|++|++|++..+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4577788889999999999999999998876554
No 110
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=89.65 E-value=0.55 Score=44.83 Aligned_cols=43 Identities=19% Similarity=0.118 Sum_probs=38.2
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCC
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQA 69 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~ 69 (318)
.-.+.+.||..+.+..|||+|.+++-..+-||.+|.|.+-++.
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~ 349 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSK 349 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCC
Confidence 3467899999999999999999999999999999999875443
No 111
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=89.53 E-value=0.41 Score=45.40 Aligned_cols=39 Identities=28% Similarity=0.399 Sum_probs=36.2
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
..+.+.||..+.+..|||+|.+++-...-||.+|.|.+.
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 568999999999999999999999999999999999753
No 112
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.58 E-value=0.35 Score=47.17 Aligned_cols=39 Identities=21% Similarity=0.400 Sum_probs=35.4
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
.....+.||.+.++.+|||+|.+|++|.+..|-+|+|..
T Consensus 485 d~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 485 DGRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred CCeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 355778899999999999999999999999999999964
No 113
>PRK13764 ATPase; Provisional
Probab=88.28 E-value=0.46 Score=48.41 Aligned_cols=40 Identities=18% Similarity=0.345 Sum_probs=36.7
Q ss_pred cceEEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 243 TSTTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 243 ~~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
......|.||.+.++.+|||+|.+|++|.+..|.+|+|..
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4567889999999999999999999999999999999964
No 114
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=88.25 E-value=0.46 Score=41.21 Aligned_cols=37 Identities=30% Similarity=0.416 Sum_probs=34.9
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEec
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 65 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~ 65 (318)
...+.||.++.+..|||+|.+++-+.+-||-++.|..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 7888999999999999999999999999999999954
No 115
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=88.15 E-value=1.2 Score=39.71 Aligned_cols=45 Identities=18% Similarity=0.341 Sum_probs=37.6
Q ss_pred EEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHH
Q 021032 32 LLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYH 87 (318)
Q Consensus 32 llVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~ 87 (318)
+.|+...+-.+|||+|+-++-|.++|+|+|-+-. ...|-|.++.+
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~ 194 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENE 194 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCc
Confidence 6788899999999999999999999999999953 34566666655
No 116
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=87.58 E-value=2.7 Score=36.83 Aligned_cols=65 Identities=15% Similarity=0.200 Sum_probs=55.2
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG 315 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~ 315 (318)
.+.+.++....-.+...+|..+++|-...||+|.+.. .+..|.|+|+...+..+...|.+++..-
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEYIEASINEILSNI 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHHHHHHHHHHHhhc
Confidence 4555566888888999999999999888899999963 5567999999999999999999988753
No 117
>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=87.49 E-value=0.66 Score=34.69 Aligned_cols=28 Identities=21% Similarity=0.551 Sum_probs=24.2
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHHh
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRAT 57 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~t 57 (318)
+++.|....-|.+|||+|.+|++|++.-
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 6777777899999999999999998653
No 118
>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=87.45 E-value=0.67 Score=33.90 Aligned_cols=35 Identities=17% Similarity=0.241 Sum_probs=28.2
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEE
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVV 279 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~ 279 (318)
....+.|..+..|.+|||.|.+++.||-....-+.
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 35667777788899999999999999998765433
No 119
>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=87.03 E-value=1.1 Score=36.95 Aligned_cols=38 Identities=24% Similarity=0.559 Sum_probs=32.0
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
+-.+.|-...-|.+|||+|.++++|..+||-+-.|...
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 34556666777999999999999999999999988654
No 120
>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=86.95 E-value=0.6 Score=36.68 Aligned_cols=30 Identities=17% Similarity=0.460 Sum_probs=26.0
Q ss_pred EEEEEEecccceeeeCCCCchHHHHHHHhC
Q 021032 29 VARLLVHSQQIGCLLGRGGHIVSEMRRATG 58 (318)
Q Consensus 29 ~~rllVp~~~vG~IIGkgG~~Ik~I~e~tG 58 (318)
.+++.|....-|.||||.|++|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 378888889999999999999999986643
No 121
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=86.03 E-value=1.6 Score=39.73 Aligned_cols=52 Identities=13% Similarity=0.277 Sum_probs=47.1
Q ss_pred ccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHHHHcC
Q 021032 257 AHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAFILCG 315 (318)
Q Consensus 257 G~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~i~~~ 315 (318)
-++||.+|++++.|.=+|.|.|-|+. .+|.+.|.-.-++.++..+.+|+.+-
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~Ni 212 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKNI 212 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhcc
Confidence 46999999999999999999999963 56999999999999999999998764
No 122
>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=84.50 E-value=1.1 Score=33.32 Aligned_cols=36 Identities=17% Similarity=0.289 Sum_probs=28.6
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEE
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVV 280 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i 280 (318)
...+|.|-...-|.|||++|.+|++|++.---...+
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 347777878888999999999999999876544444
No 123
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=84.17 E-value=1.2 Score=42.65 Aligned_cols=40 Identities=25% Similarity=0.332 Sum_probs=36.7
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
...+.+.||..+.+..|||+|.+++-...-||.+|.|.+.
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 3568899999999999999999999999999999999754
No 124
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=84.16 E-value=1 Score=40.07 Aligned_cols=37 Identities=19% Similarity=0.520 Sum_probs=30.3
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHH----HhCC-eEEE
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRR----ATGA-SIRV 63 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e----~tGa-~I~i 63 (318)
+..+++.|....-|.||||+|+.|++|++ .+|. .++|
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I 91 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQI 91 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceE
Confidence 56789999999999999999999999875 4665 3444
No 125
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=84.11 E-value=0.93 Score=44.90 Aligned_cols=39 Identities=23% Similarity=0.372 Sum_probs=36.2
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
-.+.+.||..+.+.-|||+|.+|+-..+-||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 478899999999999999999999999999999999753
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=83.07 E-value=1.3 Score=36.43 Aligned_cols=42 Identities=29% Similarity=0.261 Sum_probs=36.9
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP 285 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~ 285 (318)
..|.+|.|-.+.-|.+|||+|.++++|...+|-.-+|....+
T Consensus 75 ~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 75 DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred CCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 457888999999999999999999999999999998865444
No 127
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=82.46 E-value=2.9 Score=38.11 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=43.6
Q ss_pred eeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHHh
Q 021032 40 GCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLRE 102 (318)
Q Consensus 40 G~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~e 102 (318)
-.|||.+|+|+|.|+--|.|-|-|. -..|.+.|....+.++...|.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 5799999999999999999999984 35688999999888888887777744
No 128
>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=82.16 E-value=1.8 Score=39.45 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=25.1
Q ss_pred eeEEEEEEe-cccceeeeCCCCchHHHHHHH
Q 021032 27 AVVARLLVH-SQQIGCLLGRGGHIVSEMRRA 56 (318)
Q Consensus 27 ~~~~rllVp-~~~vG~IIGkgG~~Ik~I~e~ 56 (318)
.+...++|. .+|-+.||||+|+.||+|..+
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 366788888 479999999999999998644
No 129
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=80.74 E-value=1.5 Score=42.85 Aligned_cols=38 Identities=29% Similarity=0.343 Sum_probs=35.2
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEec
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFP 65 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~ 65 (318)
..+.+.||..+.+..|||+|.+++-...-||.+|.|.+
T Consensus 335 k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 335 RHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred cEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 45789999999999999999999999999999999953
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=78.54 E-value=3.5 Score=34.92 Aligned_cols=36 Identities=11% Similarity=0.090 Sum_probs=30.0
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcC
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVND 282 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~ 282 (318)
.+-+.|-... |.-|||+|.+|+.+++.-|-+|.+-+
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 3455565555 99999999999999999999999954
No 131
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=78.36 E-value=2 Score=33.71 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=24.1
Q ss_pred EEEEecccccccccccccchHHHHHHHhC
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQISG 275 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SG 275 (318)
.+|.|-...-|.|||++|+.|++|++.--
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 56667777789999999999999998743
No 132
>PRK15494 era GTPase Era; Provisional
Probab=77.91 E-value=2.9 Score=39.62 Aligned_cols=36 Identities=17% Similarity=0.323 Sum_probs=28.3
Q ss_pred eEEEEEEec-ccceeeeCCCCchHHHHHH--------HhCCeEEE
Q 021032 28 VVARLLVHS-QQIGCLLGRGGHIVSEMRR--------ATGASIRV 63 (318)
Q Consensus 28 ~~~rllVp~-~~vG~IIGkgG~~Ik~I~e--------~tGa~I~i 63 (318)
+...++|.. +|-+.||||+|+.||+|.. -.|++|.+
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 567888885 7999999999999999864 35665554
No 133
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=77.86 E-value=7.8 Score=38.48 Aligned_cols=39 Identities=18% Similarity=0.471 Sum_probs=33.7
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
.+-.++|-...-|.+|||+|++.++|..+||-+-.|...
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 346678888889999999999999999999988888654
No 134
>PRK00089 era GTPase Era; Reviewed
Probab=77.86 E-value=2.9 Score=38.38 Aligned_cols=36 Identities=22% Similarity=0.535 Sum_probs=27.8
Q ss_pred eEEEEEEe-cccceeeeCCCCchHHHHHHH--------hCCeEEE
Q 021032 28 VVARLLVH-SQQIGCLLGRGGHIVSEMRRA--------TGASIRV 63 (318)
Q Consensus 28 ~~~rllVp-~~~vG~IIGkgG~~Ik~I~e~--------tGa~I~i 63 (318)
+...++|. .+|-+.||||+|+.||+|..+ .|++|.+
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 56677777 478999999999999998644 5666554
No 135
>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=77.86 E-value=2.2 Score=31.78 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=22.3
Q ss_pred EEEEecccccccccccccchHHHHHHHh
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
.++.|-...-|.+||++|++|++|++.-
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 4455555777999999999999998863
No 136
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=76.85 E-value=12 Score=37.34 Aligned_cols=41 Identities=27% Similarity=0.253 Sum_probs=35.8
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP 285 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~ 285 (318)
.+.+|.|-.+.=|.||||+|++.++|.+.+|-.-+|....+
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP 139 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP 139 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC
Confidence 46788899999999999999999999999998888865444
No 137
>COG1159 Era GTPase [General function prediction only]
Probab=75.06 E-value=4 Score=37.77 Aligned_cols=37 Identities=19% Similarity=0.502 Sum_probs=28.1
Q ss_pred eeEEEEEEec-ccceeeeCCCCchHHHHH--------HHhCCeEEE
Q 021032 27 AVVARLLVHS-QQIGCLLGRGGHIVSEMR--------RATGASIRV 63 (318)
Q Consensus 27 ~~~~rllVp~-~~vG~IIGkgG~~Ik~I~--------e~tGa~I~i 63 (318)
.+...++|.. +|-|.||||+|+.||+|- +-.+++|.+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 3556678884 799999999999999885 335565554
No 138
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=71.21 E-value=8.2 Score=33.80 Aligned_cols=70 Identities=11% Similarity=0.224 Sum_probs=43.5
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc-eEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE-IVQVIGNYHSVQDALFHITSRLRETI 104 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er-~V~I~G~~~~V~~A~~~I~~~l~e~~ 104 (318)
.-.+.+-+..+..|.||||.|.++..||--+.+-+.-... -.-| .|.+-+=.+.-...+..+..++.+.+
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g--------~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV 160 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGG--------KFKRVTLDVGDYRERRKETLIKLAERAAERV 160 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcC--------cceEEEEEhhhHHHHHHHHHHHHHHHHHHHH
Confidence 3445666777779999999999999999877665543111 1122 23444444444455666666665543
No 139
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=70.48 E-value=5 Score=37.51 Aligned_cols=33 Identities=18% Similarity=0.360 Sum_probs=27.5
Q ss_pred CeeEEEEEEec-ccceeeeCCCCchHHHHHHHhC
Q 021032 26 QAVVARLLVHS-QQIGCLLGRGGHIVSEMRRATG 58 (318)
Q Consensus 26 ~~~~~rllVp~-~~vG~IIGkgG~~Ik~I~e~tG 58 (318)
-.+..++++|. ++.-.||||||..|++|-++-+
T Consensus 326 l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 326 LFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 46778999995 6788999999999999976644
No 140
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=69.97 E-value=3.9 Score=36.44 Aligned_cols=29 Identities=24% Similarity=0.297 Sum_probs=24.7
Q ss_pred eEEEEEecccccccccccccchHHHHHHH
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQI 273 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~ 273 (318)
...+|.|-...=|.||||+|++|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45777788888899999999999998764
No 141
>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=69.57 E-value=5.2 Score=34.84 Aligned_cols=31 Identities=19% Similarity=0.555 Sum_probs=26.4
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHh
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRAT 57 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~t 57 (318)
+..+++.|....-|.+||++|..|++|++.-
T Consensus 37 ~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 37 PLGTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred CCcEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 3458889999999999999999999998653
No 142
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=68.09 E-value=5.7 Score=34.95 Aligned_cols=29 Identities=24% Similarity=0.559 Sum_probs=24.8
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHHhC
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRATG 58 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~tG 58 (318)
+++.|....-|.+|||+|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 67777778899999999999999987653
No 143
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=67.61 E-value=5.6 Score=35.31 Aligned_cols=30 Identities=13% Similarity=0.352 Sum_probs=25.8
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHh
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRAT 57 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~t 57 (318)
..+++.|....-|.|||++|..|++|++.-
T Consensus 44 ~~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 44 IRTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred CcEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 347888888889999999999999998654
No 144
>CHL00048 rps3 ribosomal protein S3
Probab=67.34 E-value=6 Score=35.00 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=26.5
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHh
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRAT 57 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~t 57 (318)
...+++.|....-|.|||++|.+|++|++.-
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 3458888888889999999999999998764
No 145
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=63.94 E-value=12 Score=38.70 Aligned_cols=39 Identities=23% Similarity=0.532 Sum_probs=33.4
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecC
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPK 66 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~ 66 (318)
.+-.++|-...-|.+|||+|+++++|-.+||-+-.|...
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 345667777888999999999999999999999998754
No 146
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=61.92 E-value=8.3 Score=35.04 Aligned_cols=30 Identities=13% Similarity=0.133 Sum_probs=24.4
Q ss_pred eEEEEEecc-cccccccccccchHHHHHHHh
Q 021032 245 TTIEVVIPQ-LYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 245 ~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
....+.|.. ++-+-||||+|+.||+|...+
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 566778876 666999999999999987654
No 147
>PRK15494 era GTPase Era; Provisional
Probab=56.95 E-value=11 Score=35.65 Aligned_cols=30 Identities=23% Similarity=0.386 Sum_probs=23.8
Q ss_pred eEEEEEecc-cccccccccccchHHHHHHHh
Q 021032 245 TTIEVVIPQ-LYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 245 ~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
....+.|.. ++-+-||||+|+.||+|...+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 456778876 666999999999999886543
No 148
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=56.74 E-value=32 Score=32.65 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=44.2
Q ss_pred cccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHH
Q 021032 252 PQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIH 309 (318)
Q Consensus 252 P~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~ 309 (318)
+++.+-.+.|..|.+++.|.+..|++|... .+.++|+|+.+.+..|..+++
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR-------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC-------CceEEEEechHHHHHHHHHHh
Confidence 357778899999999999999999988873 456899999889999988887
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=56.20 E-value=12 Score=34.37 Aligned_cols=30 Identities=10% Similarity=0.153 Sum_probs=23.4
Q ss_pred eEEEEEecc-cccccccccccchHHHHHHHh
Q 021032 245 TTIEVVIPQ-LYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 245 ~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
....+.|.. +.-+-||||+|+.||+|...+
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 556677775 666999999999999876543
No 150
>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=55.68 E-value=47 Score=24.69 Aligned_cols=65 Identities=12% Similarity=0.110 Sum_probs=47.1
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC---CCCCeEEEEEcCHHHHHHHHHHHHHHHH
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP---GATEGVVMVSGTSDQMRAAQSLIHAFIL 313 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~---~~~er~v~I~Gt~~~v~~A~~lI~~~i~ 313 (318)
.+..+..-++ |-+-| =.-+.+|=+..|++++...... ..++.+++|+|+..++..|.+.+++++.
T Consensus 18 ~~a~i~are~--gV~aG--~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 18 GTATIIARED--GVLAG--LEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp EEEEEEESSS--EEE-S--HHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred EEEEEEeCCC--EEEEC--HHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 3444444443 44443 3477888888899998865433 3578999999999999999999999885
No 151
>COG1159 Era GTPase [General function prediction only]
Probab=54.00 E-value=14 Score=34.35 Aligned_cols=31 Identities=10% Similarity=0.191 Sum_probs=24.0
Q ss_pred ceEEEEEecc-cccccccccccchHHHHHHHh
Q 021032 244 STTIEVVIPQ-LYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 244 ~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
.....+.|+. ++=|-||||+|++||+|-..+
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3456677876 667999999999999886554
No 152
>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=53.89 E-value=8.7 Score=39.63 Aligned_cols=42 Identities=29% Similarity=0.254 Sum_probs=37.5
Q ss_pred ceEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCC
Q 021032 244 STTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKP 285 (318)
Q Consensus 244 ~~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~ 285 (318)
..|.+|.|-.+.-|.||||+|.++++|...+|-.-+|....+
T Consensus 92 ~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 92 DVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred CCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 467899999999999999999999999999999999876544
No 153
>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=53.45 E-value=40 Score=28.50 Aligned_cols=41 Identities=20% Similarity=0.272 Sum_probs=33.5
Q ss_pred chHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHH
Q 021032 48 HIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSR 99 (318)
Q Consensus 48 ~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~ 99 (318)
.++.+|.|-.|.-+.. ..+..|.|.|+.+.|.+|+..+...
T Consensus 126 erl~ei~E~~gvI~Ef-----------ee~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 126 ERLQEISEWHGVIFEF-----------EEDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred HHHHHHHHHhceeEEe-----------cCCcEEEEeccHHHHHHHHHHHHHH
Confidence 4567888888887776 2467899999999999999998754
No 154
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=53.13 E-value=14 Score=32.60 Aligned_cols=27 Identities=22% Similarity=0.619 Sum_probs=24.1
Q ss_pred EEEEEecccceeeeCCCCchHHHHHHH
Q 021032 30 ARLLVHSQQIGCLLGRGGHIVSEMRRA 56 (318)
Q Consensus 30 ~rllVp~~~vG~IIGkgG~~Ik~I~e~ 56 (318)
+++.|....-|.|||++|..|++|++.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~ 90 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKD 90 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHH
Confidence 778888888999999999999999854
No 155
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=52.03 E-value=13 Score=34.82 Aligned_cols=33 Identities=21% Similarity=0.299 Sum_probs=26.5
Q ss_pred ceEEEEEecc-cccccccccccchHHHHHHHhCC
Q 021032 244 STTIEVVIPQ-LYMAHVYGENNSNLSHIRQISGA 276 (318)
Q Consensus 244 ~~t~~v~IP~-~~vG~IIGk~G~~Ik~Ir~~SGA 276 (318)
.+..+|.||. +..-.||||+|..|++|-++.+-
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~ 360 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANE 360 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHH
Confidence 4678899997 55567899999999999876543
No 156
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=51.67 E-value=14 Score=32.34 Aligned_cols=69 Identities=13% Similarity=0.150 Sum_probs=43.4
Q ss_pred eEEEEEecccccccccccccchHHHHHHHhCCEEEEcCCCCCCCCeE-EEEEcC-----HHHHHHHHHHHHHHHHcCc
Q 021032 245 TTIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDPKPGATEGV-VMVSGT-----SDQMRAAQSLIHAFILCGV 316 (318)
Q Consensus 245 ~t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~~~~~~er~-v~I~Gt-----~~~v~~A~~lI~~~i~~~~ 316 (318)
.+..+.|-.+..|.+||+.|.+++.||-.+.+.+.- ..+..-|+ |-+-+- ..=+..|+.+-...++.++
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~---~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~~tg~ 165 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK---IGGKFKRVTLDVGDYRERRKETLIKLAERAAERVLETGR 165 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh---hcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 467788888889999999999999999988654433 22222332 222222 2334556666655555554
No 157
>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=49.52 E-value=16 Score=31.90 Aligned_cols=29 Identities=14% Similarity=0.132 Sum_probs=24.0
Q ss_pred EEEEEecccccccccccccchHHHHHHHh
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
..++.|-...-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46677777778999999999999988763
No 158
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=49.11 E-value=15 Score=32.29 Aligned_cols=30 Identities=17% Similarity=0.204 Sum_probs=23.3
Q ss_pred EEEEecccccccccccccchHHHHHHHhCC
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQISGA 276 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA 276 (318)
.++.|-...-|.+||++|++|+++++.-.-
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 444455577899999999999999987543
No 159
>CHL00048 rps3 ribosomal protein S3
Probab=47.44 E-value=18 Score=32.04 Aligned_cols=29 Identities=10% Similarity=0.126 Sum_probs=24.0
Q ss_pred EEEEEecccccccccccccchHHHHHHHh
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
..+|.|-...-|.|||++|.+|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46666767778999999999999998864
No 160
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=45.32 E-value=19 Score=32.06 Aligned_cols=29 Identities=14% Similarity=0.329 Sum_probs=23.6
Q ss_pred EEEEEecccccccccccccchHHHHHHHh
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
..+|.|-...-|.|||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 36666767777999999999999998764
No 161
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=41.15 E-value=26 Score=31.42 Aligned_cols=30 Identities=20% Similarity=0.509 Sum_probs=24.4
Q ss_pred eEEEEEEecccceeeeCCCCchHHHHHHHh
Q 021032 28 VVARLLVHSQQIGCLLGRGGHIVSEMRRAT 57 (318)
Q Consensus 28 ~~~rllVp~~~vG~IIGkgG~~Ik~I~e~t 57 (318)
-.+++.|....-|.|||++|..|++|++.-
T Consensus 62 ~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L 91 (232)
T PRK00310 62 KRVRVTIHTARPGIVIGKKGAEIEKLRKEL 91 (232)
T ss_pred CeEEEEEEECCCccccCCCcHHHHHHHHHH
Confidence 346677777788999999999999998654
No 162
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=40.84 E-value=78 Score=24.78 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=25.1
Q ss_pred CceEEEEecHHHHHHHHHHHHHHHHhhc
Q 021032 77 DEIVQVIGNYHSVQDALFHITSRLRETI 104 (318)
Q Consensus 77 er~V~I~G~~~~V~~A~~~I~~~l~e~~ 104 (318)
...|.|+|+..+|+.|+..|.+.+++.+
T Consensus 74 sGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 74 SGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred ceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 3569999999999999999999999864
No 163
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.73 E-value=85 Score=25.96 Aligned_cols=43 Identities=21% Similarity=0.307 Sum_probs=33.3
Q ss_pred chHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHH
Q 021032 48 HIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 101 (318)
Q Consensus 48 ~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~ 101 (318)
+.++.|.|-.|.-|.+. ...+|.|.|+.+.|.+|+..|...-+
T Consensus 126 eRlqDi~E~hgvIiE~~-----------E~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFE-----------EYDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEee-----------eccEEEEeccHHHHHHHHHHHHHHHh
Confidence 35566677777777763 35789999999999999999977643
No 164
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=39.71 E-value=23 Score=35.33 Aligned_cols=74 Identities=8% Similarity=0.060 Sum_probs=54.5
Q ss_pred eeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCc-eEEEEecH---HHHHHHHHHHHHHHHh
Q 021032 27 AVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDE-IVQVIGNY---HSVQDALFHITSRLRE 102 (318)
Q Consensus 27 ~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er-~V~I~G~~---~~V~~A~~~I~~~l~e 102 (318)
+-++.+.||.+.+-.|||-||..|++++.+-++.|++.-.-..|. +..+ .|.|.-+. +++.-+...+.+++.+
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---SQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---hhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 345889999999999999999999999999999999864322332 2323 37777755 4555666677777776
Q ss_pred h
Q 021032 103 T 103 (318)
Q Consensus 103 ~ 103 (318)
.
T Consensus 525 ~ 525 (657)
T COG5166 525 Q 525 (657)
T ss_pred h
Confidence 5
No 165
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=34.67 E-value=35 Score=30.08 Aligned_cols=28 Identities=25% Similarity=0.300 Sum_probs=23.0
Q ss_pred EEEEecccccccccccccchHHHHHHHh
Q 021032 247 IEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 247 ~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
.+|.|-...-|.|||++|.+|++|++.-
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 5666767777999999999999998653
No 166
>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=33.56 E-value=52 Score=22.70 Aligned_cols=49 Identities=16% Similarity=0.238 Sum_probs=31.0
Q ss_pred CchHHH--HHHHhCCeEEEecCCC---CCCC--CCCCCceEEEEecHHHHHHHHHH
Q 021032 47 GHIVSE--MRRATGASIRVFPKDQ---APRC--GSPHDEIVQVIGNYHSVQDALFH 95 (318)
Q Consensus 47 G~~Ik~--I~e~tGa~I~i~~~~~---~p~~--~~~~er~V~I~G~~~~V~~A~~~ 95 (318)
|.+|++ +++.+++.|--...+. .|.. .-.....|.+.|+.+.+.++...
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 457889 8888898875543322 1211 01234678999999999877654
No 167
>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=31.85 E-value=1.5e+02 Score=21.94 Aligned_cols=71 Identities=20% Similarity=0.223 Sum_probs=47.4
Q ss_pred CCeeEEEEEEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHHHHHH
Q 021032 25 GQAVVARLLVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHITSRLR 101 (318)
Q Consensus 25 ~~~~~~rllVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~~~l~ 101 (318)
+...+..+. ..+-|.+= |=.-++++=+..|+++....+|.-. -...+.++++.|+..++..|.+.+...|.
T Consensus 15 ~~~~~a~i~--are~gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~--v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 15 DKTGTATII--AREDGVLA--GLEEAEEIFEKLGLEVEWLVKDGDR--VEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp TSEEEEEEE--ESSSEEE---SHHHHHHHHHHCTEEEEESS-TT-E--EETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEE--eCCCEEEE--CHHHHHHHHhhccEEEEEEeCCCCC--ccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 344444443 34445554 4457788888889999876443321 12457899999999999999998888775
No 168
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=31.76 E-value=1.5e+02 Score=28.25 Aligned_cols=53 Identities=26% Similarity=0.252 Sum_probs=43.7
Q ss_pred EEecccceeeeCCCCchHHHHHHHhCCeEEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHHHH
Q 021032 33 LVHSQQIGCLLGRGGHIVSEMRRATGASIRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFHIT 97 (318)
Q Consensus 33 lVp~~~vG~IIGkgG~~Ik~I~e~tGa~I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~I~ 97 (318)
+-+.+.+-.|.|..|.+++-|++..|++|... .+.+.|+|+...|..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 33467888999999999999999999988862 467899999777777777666
No 169
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=30.60 E-value=63 Score=23.11 Aligned_cols=33 Identities=21% Similarity=0.495 Sum_probs=24.9
Q ss_pred hCCEEEEcCCCCCCCCeEEEEEcCHHHHHHHHHHHHHH
Q 021032 274 SGANVVVNDPKPGATEGVVMVSGTSDQMRAAQSLIHAF 311 (318)
Q Consensus 274 SGA~I~i~~~~~~~~er~v~I~Gt~~~v~~A~~lI~~~ 311 (318)
.+.+|..+. .-..|.|+|+++.++..+.||..+
T Consensus 44 ~~~~i~~d~-----~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 44 SSGRIVADE-----RTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEEC-----TTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCeEEEEEC-----CCCEEEEEeCHHHHHHHHHHHHHH
Confidence 344666643 345689999999999999999765
No 170
>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=25.68 E-value=1.3e+02 Score=21.55 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=24.5
Q ss_pred CCceEEEEecHHHHHHHHHHHHHHHHhh
Q 021032 76 HDEIVQVIGNYHSVQDALFHITSRLRET 103 (318)
Q Consensus 76 ~er~V~I~G~~~~V~~A~~~I~~~l~e~ 103 (318)
..-.+.|+|+..+|+.|+....+.+.+.
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 3567889999999999999999988874
No 171
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.07 E-value=99 Score=21.09 Aligned_cols=22 Identities=27% Similarity=0.366 Sum_probs=19.2
Q ss_pred CHHHHHHHHHHHHHHHHcCcCC
Q 021032 297 TSDQMRAAQSLIHAFILCGVTS 318 (318)
Q Consensus 297 t~~~v~~A~~lI~~~i~~~~~~ 318 (318)
|-++-+.|..-|++++.+|-||
T Consensus 9 tHeqQQ~AVE~Iq~lMaeGmSs 30 (60)
T COG3140 9 THEQQQKAVERIQELMAEGMSS 30 (60)
T ss_pred cHHHHHHHHHHHHHHHHccccc
Confidence 5688899999999999998876
No 172
>PRK06106 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=24.74 E-value=5.6e+02 Score=23.65 Aligned_cols=74 Identities=18% Similarity=0.133 Sum_probs=47.9
Q ss_pred CeeEEEEEEecccc--eeeeCCC------CchHHHHHHHhCCe--EEEecCCCCCCCCCCCCceEEEEecHHHHHHHHHH
Q 021032 26 QAVVARLLVHSQQI--GCLLGRG------GHIVSEMRRATGAS--IRVFPKDQAPRCGSPHDEIVQVIGNYHSVQDALFH 95 (318)
Q Consensus 26 ~~~~~rllVp~~~v--G~IIGkg------G~~Ik~I~e~tGa~--I~i~~~~~~p~~~~~~er~V~I~G~~~~V~~A~~~ 95 (318)
..+|.+.++|.+.. ..|+=|. -.-.+++-+..|.. +.+..++.-. -...+.+++++|+...+..+.+.
T Consensus 27 gDlTt~~l~~~~~~~~~~i~ake~gv~aG~~~a~~vf~~~~~~~~~~~~~~dG~~--v~~g~~i~~i~G~a~~ll~~ER~ 104 (281)
T PRK06106 27 GDITSDAIVPADHRATVVLVARQPGVIAGLDLARLAFRLVDPEIEMRRHLPDGAA--VAPGDVIATISGPARGLLTAERT 104 (281)
T ss_pred CCCCcccccCCCCeEEEEEEecCCeEEECHHHHHHHHHHhCCceEEEEEeCCCCE--EcCCCEEEEEEECHHHHHHHHHH
Confidence 46677777766543 3555553 33457888888866 4444332211 12468899999999999988887
Q ss_pred HHHHHH
Q 021032 96 ITSRLR 101 (318)
Q Consensus 96 I~~~l~ 101 (318)
+...|.
T Consensus 105 ~LN~L~ 110 (281)
T PRK06106 105 ALNFLC 110 (281)
T ss_pred HHHHHH
Confidence 766663
No 173
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=24.42 E-value=72 Score=28.57 Aligned_cols=29 Identities=17% Similarity=0.277 Sum_probs=22.5
Q ss_pred EEEEEecccccccccccccchHHHHHHHh
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQIS 274 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~S 274 (318)
..+|.|-...-|.|||++|.+|++|++.-
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 35555555667899999999999988764
No 174
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=23.27 E-value=1.7e+02 Score=20.66 Aligned_cols=52 Identities=13% Similarity=0.195 Sum_probs=33.2
Q ss_pred CchHHHHHHHhCCeEEEecCCCCCCC-CCCCCceEEEEecHHHHHHHHHHHHH
Q 021032 47 GHIVSEMRRATGASIRVFPKDQAPRC-GSPHDEIVQVIGNYHSVQDALFHITS 98 (318)
Q Consensus 47 G~~Ik~I~e~tGa~I~i~~~~~~p~~-~~~~er~V~I~G~~~~V~~A~~~I~~ 98 (318)
.--|.++..+++..+.|....--.-. ..-..=+|.+.|+.+.+.+|+..+.+
T Consensus 16 ~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~ 68 (76)
T PF09383_consen 16 EPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLRE 68 (76)
T ss_dssp SCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHH
T ss_pred chHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHH
Confidence 34688999999999999753110000 00112368899999999999888764
No 175
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=22.97 E-value=1.7e+02 Score=22.68 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=25.0
Q ss_pred CCCeEEEEEc-CHHHHHHHHHHHHHHHHcC
Q 021032 287 ATEGVVMVSG-TSDQMRAAQSLIHAFILCG 315 (318)
Q Consensus 287 ~~er~v~I~G-t~~~v~~A~~lI~~~i~~~ 315 (318)
+.+-++.|.| ++.+|+.|...+.+.+++.
T Consensus 71 sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 71 AGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred CccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 5666778999 9999999999999998874
No 176
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=21.95 E-value=1e+02 Score=21.60 Aligned_cols=21 Identities=19% Similarity=0.264 Sum_probs=17.8
Q ss_pred ceEEEEecHHHHHHHHHHHHH
Q 021032 78 EIVQVIGNYHSVQDALFHITS 98 (318)
Q Consensus 78 r~V~I~G~~~~V~~A~~~I~~ 98 (318)
-.+.|+|+.++|+.|+..|.+
T Consensus 39 ~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 39 ITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred EEEEEEecHHHHHHHHHHHhh
Confidence 356789999999999998864
No 177
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=20.52 E-value=54 Score=32.77 Aligned_cols=38 Identities=8% Similarity=0.098 Sum_probs=34.1
Q ss_pred EEEEEecccccccccccccchHHHHHHHhCCEEEEcCC
Q 021032 246 TIEVVIPQLYMAHVYGENNSNLSHIRQISGANVVVNDP 283 (318)
Q Consensus 246 t~~v~IP~~~vG~IIGk~G~~Ik~Ir~~SGA~I~i~~~ 283 (318)
...+.||...+-.|||.||..|.++....+..|++.+.
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~ 487 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNF 487 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhh
Confidence 35678999999999999999999999999999998653
Done!