Query psy11278
Match_columns 238
No_of_seqs 129 out of 1454
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 22:46:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11278.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11278hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1676|consensus 100.0 3.9E-28 8.5E-33 214.0 18.1 218 2-222 142-390 (600)
2 KOG2193|consensus 99.9 6.2E-27 1.3E-31 198.3 11.1 230 1-235 201-503 (584)
3 KOG1676|consensus 99.9 1.3E-25 2.8E-30 198.1 16.8 214 2-221 57-300 (600)
4 KOG2193|consensus 99.9 1.6E-24 3.4E-29 183.8 11.3 214 1-219 282-562 (584)
5 KOG2192|consensus 99.9 3E-23 6.6E-28 166.9 17.6 211 1-220 50-383 (390)
6 KOG2191|consensus 99.9 1.4E-20 2.9E-25 155.6 15.2 164 1-221 41-204 (402)
7 KOG2190|consensus 99.8 1.3E-18 2.8E-23 155.4 14.9 214 1-220 140-408 (485)
8 TIGR03665 arCOG04150 arCOG0415 99.7 7.3E-17 1.6E-21 126.7 10.2 147 3-222 2-152 (172)
9 PRK13763 putative RNA-processi 99.7 4.2E-16 9.1E-21 123.2 11.7 147 2-222 6-158 (180)
10 KOG2190|consensus 99.7 5E-16 1.1E-20 138.8 13.3 156 1-222 45-209 (485)
11 cd02394 vigilin_like_KH K homo 99.5 3.2E-14 7E-19 93.0 6.1 59 2-65 3-61 (62)
12 cd02396 PCBP_like_KH K homolog 99.5 6.9E-14 1.5E-18 92.3 6.7 63 1-65 2-64 (65)
13 cd02394 vigilin_like_KH K homo 99.5 5.3E-14 1.1E-18 92.0 5.9 61 150-216 2-62 (62)
14 cd02396 PCBP_like_KH K homolog 99.4 4.2E-13 9.1E-18 88.5 7.2 63 150-215 2-64 (65)
15 PF00013 KH_1: KH domain syndr 99.4 1E-13 2.2E-18 90.0 2.9 60 149-215 1-60 (60)
16 cd02393 PNPase_KH Polynucleoti 99.4 6.5E-13 1.4E-17 86.3 6.7 55 2-65 5-60 (61)
17 PF00013 KH_1: KH domain syndr 99.4 1.9E-13 4.1E-18 88.7 2.9 59 1-65 2-60 (60)
18 cd02393 PNPase_KH Polynucleoti 99.4 2.9E-12 6.2E-17 83.3 7.4 58 149-216 3-61 (61)
19 cd00105 KH-I K homology RNA-bi 99.4 3.1E-12 6.6E-17 84.0 7.5 63 150-216 2-64 (64)
20 cd00105 KH-I K homology RNA-bi 99.3 4.1E-12 8.9E-17 83.3 7.3 61 2-65 3-63 (64)
21 KOG2192|consensus 99.3 1.8E-11 3.9E-16 99.3 8.8 133 81-220 60-192 (390)
22 PF13014 KH_3: KH domain 99.2 6E-11 1.3E-15 71.5 4.9 43 9-53 1-43 (43)
23 KOG2208|consensus 99.1 1.3E-10 2.7E-15 109.8 8.3 202 2-219 350-560 (753)
24 KOG2208|consensus 99.1 2.5E-10 5.5E-15 107.8 10.2 218 2-233 204-428 (753)
25 smart00322 KH K homology RNA-b 99.1 2.9E-10 6.3E-15 74.9 7.7 63 2-69 6-68 (69)
26 smart00322 KH K homology RNA-b 99.1 5.9E-10 1.3E-14 73.4 8.5 66 148-219 3-68 (69)
27 PF13014 KH_3: KH domain 99.1 1.9E-10 4.1E-15 69.3 5.2 43 158-203 1-43 (43)
28 COG1094 Predicted RNA-binding 99.0 2.3E-08 5E-13 78.4 14.0 152 2-224 11-167 (194)
29 KOG2191|consensus 98.8 1.8E-08 3.9E-13 84.3 6.7 69 2-70 135-203 (402)
30 cd02395 SF1_like-KH Splicing f 98.7 5.5E-08 1.2E-12 71.6 7.6 70 2-71 3-95 (120)
31 KOG2279|consensus 98.6 9.4E-08 2E-12 84.9 7.1 213 2-219 71-366 (608)
32 KOG2113|consensus 98.6 4.3E-08 9.2E-13 81.4 3.9 151 2-219 29-181 (394)
33 TIGR03665 arCOG04150 arCOG0415 98.5 2.5E-07 5.5E-12 72.7 5.2 52 9-70 99-150 (172)
34 PRK13763 putative RNA-processi 98.4 4.7E-07 1E-11 71.7 5.5 63 149-220 4-70 (180)
35 cd02395 SF1_like-KH Splicing f 98.4 2E-06 4.3E-11 63.4 7.5 65 157-221 15-95 (120)
36 TIGR02696 pppGpp_PNP guanosine 98.2 4.5E-06 9.8E-11 78.1 6.8 60 2-70 581-641 (719)
37 KOG2814|consensus 97.9 1.2E-05 2.6E-10 67.8 4.2 64 3-71 61-125 (345)
38 TIGR02696 pppGpp_PNP guanosine 97.9 6.2E-05 1.3E-09 70.7 9.0 87 124-220 548-641 (719)
39 TIGR03591 polynuc_phos polyrib 97.9 1.7E-05 3.6E-10 75.0 5.3 60 2-70 554-614 (684)
40 TIGR03591 polynuc_phos polyrib 97.7 0.00013 2.8E-09 69.1 7.8 86 125-220 521-614 (684)
41 COG1094 Predicted RNA-binding 97.6 0.00015 3.2E-09 57.2 5.7 53 9-71 112-164 (194)
42 KOG0119|consensus 97.5 0.00016 3.5E-09 64.0 5.6 64 8-71 153-230 (554)
43 KOG2279|consensus 97.5 9E-05 2E-09 66.4 3.9 126 83-219 82-207 (608)
44 KOG2113|consensus 97.5 0.0001 2.2E-09 61.7 3.3 63 148-217 26-88 (394)
45 PLN00207 polyribonucleotide nu 97.4 0.00034 7.4E-09 67.2 6.3 87 124-220 654-749 (891)
46 PLN00207 polyribonucleotide nu 97.4 0.00014 3E-09 69.9 3.6 60 2-70 688-749 (891)
47 cd02134 NusA_KH NusA_K homolog 97.2 0.0004 8.6E-09 44.9 3.4 33 2-34 28-60 (61)
48 PF14611 SLS: Mitochondrial in 97.2 0.0081 1.8E-07 48.7 11.8 105 3-119 30-142 (210)
49 PRK08406 transcription elongat 97.2 0.0023 5.1E-08 48.5 7.9 34 150-183 101-134 (140)
50 KOG2814|consensus 97.2 0.00033 7.2E-09 59.3 3.5 75 149-229 58-136 (345)
51 COG1185 Pnp Polyribonucleotide 97.2 0.00052 1.1E-08 63.5 5.0 61 2-71 555-616 (692)
52 KOG0336|consensus 97.2 0.00033 7.1E-09 61.3 3.3 58 3-66 51-108 (629)
53 KOG0336|consensus 97.1 0.00037 7.9E-09 61.0 3.1 63 150-219 49-111 (629)
54 PRK04163 exosome complex RNA-b 97.1 0.0011 2.3E-08 54.8 5.3 62 2-72 148-210 (235)
55 PRK00106 hypothetical protein; 97.0 0.0014 2.9E-08 60.2 6.3 60 2-69 228-289 (535)
56 TIGR03319 YmdA_YtgF conserved 97.0 0.0014 3E-08 60.2 6.2 60 2-69 207-268 (514)
57 PRK00106 hypothetical protein; 97.0 0.0046 1E-07 56.8 8.9 73 137-219 215-289 (535)
58 COG1185 Pnp Polyribonucleotide 96.9 0.0032 7E-08 58.4 7.7 96 114-219 506-614 (692)
59 PRK12704 phosphodiesterase; Pr 96.9 0.0022 4.8E-08 58.9 6.7 60 2-69 213-274 (520)
60 PRK12704 phosphodiesterase; Pr 96.9 0.0044 9.5E-08 57.0 8.6 61 150-219 212-274 (520)
61 TIGR03319 YmdA_YtgF conserved 96.9 0.0043 9.4E-08 57.0 8.4 61 150-219 206-268 (514)
62 PRK11824 polynucleotide phosph 96.9 0.00079 1.7E-08 64.0 3.6 60 2-70 557-617 (693)
63 KOG0119|consensus 96.7 0.0058 1.3E-07 54.5 7.3 66 156-221 152-230 (554)
64 KOG1588|consensus 96.7 0.002 4.4E-08 53.0 3.9 38 2-39 95-138 (259)
65 PRK11824 polynucleotide phosph 96.6 0.004 8.6E-08 59.3 6.3 87 125-221 524-618 (693)
66 cd02134 NusA_KH NusA_K homolog 96.6 0.004 8.6E-08 40.1 4.4 34 150-183 27-60 (61)
67 PRK04163 exosome complex RNA-b 96.4 0.0062 1.3E-07 50.3 5.2 62 150-221 147-209 (235)
68 PF14611 SLS: Mitochondrial in 96.2 0.12 2.5E-06 41.9 11.4 113 86-220 43-164 (210)
69 PRK12705 hypothetical protein; 96.1 0.0051 1.1E-07 56.1 3.5 59 3-69 202-262 (508)
70 KOG1067|consensus 96.1 0.018 3.8E-07 52.5 6.7 95 124-229 566-668 (760)
71 COG5166 Uncharacterized conser 96.0 0.025 5.4E-07 50.9 6.9 113 12-130 393-514 (657)
72 KOG1588|consensus 95.9 0.012 2.6E-07 48.6 4.6 72 148-219 92-189 (259)
73 PRK12705 hypothetical protein; 95.9 0.02 4.2E-07 52.4 6.3 79 132-220 183-263 (508)
74 PRK00468 hypothetical protein; 95.2 0.014 3E-07 39.3 2.1 26 2-27 33-58 (75)
75 PRK02821 hypothetical protein; 95.1 0.015 3.3E-07 39.2 2.0 28 2-29 34-61 (77)
76 COG5176 MSL5 Splicing factor ( 95.0 0.03 6.5E-07 44.6 3.8 32 7-38 162-193 (269)
77 COG1837 Predicted RNA-binding 95.0 0.018 4E-07 38.6 2.2 25 2-26 33-57 (76)
78 PRK01064 hypothetical protein; 94.7 0.029 6.2E-07 38.0 2.5 26 2-27 33-58 (78)
79 COG5176 MSL5 Splicing factor ( 94.0 0.094 2E-06 41.8 4.5 32 156-187 162-193 (269)
80 KOG4369|consensus 94.0 0.022 4.7E-07 55.9 1.0 64 2-67 1343-1406(2131)
81 KOG2874|consensus 93.4 0.13 2.8E-06 42.9 4.5 52 10-71 160-211 (356)
82 PRK00468 hypothetical protein; 93.3 0.11 2.4E-06 34.9 3.3 32 148-179 30-61 (75)
83 KOG1067|consensus 93.3 0.087 1.9E-06 48.1 3.5 59 2-70 600-659 (760)
84 KOG2874|consensus 93.3 0.13 2.8E-06 42.9 4.3 55 160-225 161-215 (356)
85 cd02409 KH-II KH-II (K homolo 93.0 0.13 2.7E-06 33.1 3.2 28 5-32 31-58 (68)
86 PRK02821 hypothetical protein; 92.8 0.13 2.9E-06 34.7 3.1 33 148-180 31-63 (77)
87 COG1837 Predicted RNA-binding 92.8 0.19 4.1E-06 33.8 3.7 31 147-177 29-59 (76)
88 PF13184 KH_5: NusA-like KH do 92.7 0.094 2E-06 34.6 2.2 28 10-37 19-47 (69)
89 COG1097 RRP4 RNA-binding prote 92.5 0.31 6.8E-06 39.9 5.4 59 3-70 150-209 (239)
90 PRK01064 hypothetical protein; 92.5 0.26 5.6E-06 33.3 4.2 33 147-179 29-61 (78)
91 PF13083 KH_4: KH domain; PDB: 92.4 0.035 7.7E-07 37.0 -0.1 28 2-29 32-59 (73)
92 TIGR01952 nusA_arch NusA famil 91.8 0.2 4.3E-06 38.0 3.3 34 150-183 102-135 (141)
93 COG1855 ATPase (PilT family) [ 91.3 0.11 2.3E-06 46.7 1.6 37 2-38 489-525 (604)
94 cd02414 jag_KH jag_K homology 91.3 0.19 4.2E-06 33.8 2.5 33 2-34 27-59 (77)
95 COG5166 Uncharacterized conser 90.9 1.2 2.6E-05 40.5 7.7 36 150-185 451-486 (657)
96 PRK13764 ATPase; Provisional 90.8 0.14 3.1E-06 47.9 2.0 37 2-38 484-520 (602)
97 KOG3273|consensus 90.6 0.18 3.8E-06 40.1 2.0 50 9-68 179-228 (252)
98 PRK08406 transcription elongat 90.4 0.35 7.5E-06 36.6 3.5 36 150-185 34-69 (140)
99 COG1097 RRP4 RNA-binding prote 90.4 0.77 1.7E-05 37.7 5.6 47 150-206 148-194 (239)
100 PF07650 KH_2: KH domain syndr 90.1 0.1 2.2E-06 35.1 0.3 31 3-33 29-59 (78)
101 KOG4369|consensus 88.7 0.18 3.8E-06 49.9 0.9 67 150-219 1342-1408(2131)
102 PRK06418 transcription elongat 88.6 0.47 1E-05 36.9 3.0 34 3-37 65-98 (166)
103 cd02413 40S_S3_KH K homology R 88.6 0.23 4.9E-06 33.9 1.1 35 2-36 33-67 (81)
104 KOG3273|consensus 88.5 0.28 6.1E-06 39.0 1.7 56 158-224 179-234 (252)
105 cd02410 archeal_CPSF_KH The ar 88.5 0.8 1.7E-05 34.7 4.1 87 86-183 23-111 (145)
106 PF13184 KH_5: NusA-like KH do 88.2 0.27 6E-06 32.4 1.3 37 151-187 6-48 (69)
107 PRK12328 nusA transcription el 87.9 0.39 8.4E-06 42.2 2.4 37 2-38 311-347 (374)
108 cd02409 KH-II KH-II (K homolo 86.8 1.3 2.8E-05 28.2 4.0 32 150-181 27-58 (68)
109 cd02414 jag_KH jag_K homology 85.9 1.1 2.3E-05 30.1 3.3 34 150-183 26-59 (77)
110 PF13083 KH_4: KH domain; PDB: 85.7 0.23 5E-06 33.0 -0.1 32 150-181 31-62 (73)
111 TIGR01952 nusA_arch NusA famil 85.7 0.85 1.8E-05 34.5 2.9 36 150-185 35-70 (141)
112 PRK09202 nusA transcription el 85.6 0.6 1.3E-05 42.6 2.4 36 2-37 305-340 (470)
113 COG1855 ATPase (PilT family) [ 85.1 0.52 1.1E-05 42.5 1.8 37 150-186 488-524 (604)
114 cd02413 40S_S3_KH K homology R 83.9 0.75 1.6E-05 31.3 1.8 36 150-185 32-67 (81)
115 PRK13764 ATPase; Provisional 83.5 0.78 1.7E-05 43.1 2.3 36 150-185 483-518 (602)
116 PF07650 KH_2: KH domain syndr 82.9 0.31 6.7E-06 32.7 -0.4 33 150-182 27-59 (78)
117 COG1782 Predicted metal-depend 82.5 10 0.00022 34.9 8.6 115 57-182 6-133 (637)
118 TIGR01953 NusA transcription t 82.4 1.3 2.9E-05 38.6 3.2 36 150-185 303-338 (341)
119 COG0195 NusA Transcription elo 81.9 1.2 2.6E-05 35.5 2.4 88 83-185 90-179 (190)
120 PRK12328 nusA transcription el 81.3 1.4 3.1E-05 38.8 2.9 38 150-187 310-347 (374)
121 PRK12329 nusA transcription el 80.6 1.2 2.7E-05 39.9 2.4 35 2-36 338-372 (449)
122 COG0195 NusA Transcription elo 80.5 1.5 3.2E-05 35.0 2.5 83 5-106 82-179 (190)
123 cd02412 30S_S3_KH K homology R 80.4 1.3 2.8E-05 31.9 2.1 30 2-31 64-93 (109)
124 cd02411 archeal_30S_S3_KH K ho 80.2 1.6 3.5E-05 29.9 2.4 27 2-28 41-67 (85)
125 PRK12327 nusA transcription el 79.8 1.8 4E-05 38.1 3.2 38 150-187 305-342 (362)
126 TIGR01953 NusA transcription t 79.0 11 0.00024 32.9 7.7 84 9-106 244-338 (341)
127 PRK09202 nusA transcription el 78.0 1.9 4.1E-05 39.4 2.7 36 150-185 304-339 (470)
128 COG1702 PhoH Phosphate starvat 77.8 6.3 0.00014 34.3 5.7 50 7-66 23-72 (348)
129 cd02410 archeal_CPSF_KH The ar 77.5 3.2 7E-05 31.4 3.4 34 3-36 80-113 (145)
130 COG0092 RpsC Ribosomal protein 76.6 2.5 5.4E-05 34.7 2.8 28 2-29 54-81 (233)
131 COG1702 PhoH Phosphate starvat 75.7 6.1 0.00013 34.4 5.1 54 155-219 22-77 (348)
132 PRK12329 nusA transcription el 74.0 2.9 6.3E-05 37.6 2.8 36 150-185 337-372 (449)
133 PRK06418 transcription elongat 73.4 4 8.7E-05 31.8 3.1 36 151-187 64-99 (166)
134 TIGR03675 arCOG00543 arCOG0054 72.2 19 0.00042 34.3 7.9 112 61-183 4-128 (630)
135 cd02411 archeal_30S_S3_KH K ho 71.2 4.3 9.3E-05 27.8 2.6 29 150-178 40-68 (85)
136 cd02412 30S_S3_KH K homology R 69.7 3.6 7.9E-05 29.6 2.1 31 150-180 63-93 (109)
137 PRK15494 era GTPase Era; Provi 63.0 6.8 0.00015 34.1 2.8 24 3-26 277-301 (339)
138 COG0092 RpsC Ribosomal protein 60.7 8.3 0.00018 31.7 2.7 28 150-177 53-80 (233)
139 PRK00089 era GTPase Era; Revie 60.6 5.4 0.00012 33.7 1.7 24 3-26 230-254 (292)
140 COG1159 Era GTPase [General fu 59.1 6.1 0.00013 33.7 1.7 23 3-25 233-256 (298)
141 PRK15468 carboxysome structura 58.9 15 0.00032 26.4 3.3 32 45-76 73-104 (111)
142 PRK12327 nusA transcription el 58.7 8.4 0.00018 34.0 2.6 85 9-106 246-340 (362)
143 TIGR00436 era GTP-binding prot 58.3 16 0.00034 30.6 4.2 30 148-177 221-251 (270)
144 COG1847 Jag Predicted RNA-bind 56.3 7.4 0.00016 31.3 1.7 33 2-34 94-126 (208)
145 PF02080 TrkA_C: TrkA-C domain 55.2 25 0.00054 22.4 3.9 48 18-65 14-70 (71)
146 cd00652 TBP_TLF TATA box bindi 53.4 1.1E+02 0.0023 24.0 9.4 25 45-69 54-80 (174)
147 PRK15494 era GTPase Era; Provi 53.3 21 0.00046 31.1 4.2 28 149-176 274-302 (339)
148 PRK00089 era GTPase Era; Revie 53.3 21 0.00046 30.1 4.2 29 149-177 227-256 (292)
149 COG1782 Predicted metal-depend 52.3 13 0.00028 34.2 2.7 34 3-36 103-136 (637)
150 PF09869 DUF2096: Uncharacteri 51.2 45 0.00098 25.9 5.2 41 19-68 126-166 (169)
151 COG4810 EutS Ethanolamine util 50.5 23 0.00051 25.0 3.2 34 45-78 83-116 (121)
152 TIGR01008 rpsC_E_A ribosomal p 50.4 14 0.00031 29.6 2.5 29 2-30 41-69 (195)
153 COG1847 Jag Predicted RNA-bind 49.7 22 0.00048 28.7 3.4 34 150-183 93-126 (208)
154 PRK04191 rps3p 30S ribosomal p 49.5 16 0.00035 29.5 2.7 30 2-31 43-72 (207)
155 CHL00048 rps3 ribosomal protei 49.2 16 0.00035 29.7 2.6 29 2-30 69-97 (214)
156 TIGR03802 Asp_Ala_antiprt aspa 49.0 1.6E+02 0.0035 27.7 9.6 111 18-129 232-374 (562)
157 cd07055 BMC_like_2 Bacterial M 48.5 48 0.001 21.2 4.1 21 47-67 39-59 (61)
158 COG1159 Era GTPase [General fu 48.2 25 0.00054 30.1 3.7 28 149-176 230-258 (298)
159 PTZ00084 40S ribosomal protein 47.4 17 0.00037 29.7 2.5 32 2-33 47-78 (220)
160 KOG1423|consensus 46.2 31 0.00067 29.9 3.9 32 149-180 329-361 (379)
161 PRK15468 carboxysome structura 45.1 31 0.00067 24.7 3.2 44 177-232 63-106 (111)
162 COG4010 Uncharacterized protei 44.1 60 0.0013 24.7 4.7 41 19-68 126-166 (170)
163 PF03958 Secretin_N: Bacterial 43.1 74 0.0016 20.9 4.9 24 45-68 53-76 (82)
164 TIGR03802 Asp_Ala_antiprt aspa 41.9 2.4E+02 0.0051 26.6 9.5 122 87-216 231-377 (562)
165 PRK11895 ilvH acetolactate syn 40.9 1.7E+02 0.0037 22.6 8.9 78 48-128 47-135 (161)
166 cd04516 TBP_eukaryotes eukaryo 40.7 1.8E+02 0.0038 22.8 9.2 25 45-69 54-80 (174)
167 COG4010 Uncharacterized protei 40.3 77 0.0017 24.1 4.8 41 168-218 126-166 (170)
168 TIGR03675 arCOG00543 arCOG0054 39.8 32 0.00069 32.8 3.5 34 3-36 97-130 (630)
169 PF10369 ALS_ss_C: Small subun 39.5 71 0.0015 21.1 4.2 44 167-218 16-59 (75)
170 PRK11895 ilvH acetolactate syn 38.8 1.6E+02 0.0036 22.7 6.7 110 92-218 20-141 (161)
171 PRK04191 rps3p 30S ribosomal p 38.7 31 0.00068 27.9 2.8 30 150-179 42-71 (207)
172 PF09869 DUF2096: Uncharacteri 38.7 95 0.0021 24.2 5.2 41 168-218 126-166 (169)
173 CHL00100 ilvH acetohydroxyacid 38.1 2E+02 0.0043 22.6 9.1 94 114-218 47-141 (174)
174 CHL00048 rps3 ribosomal protei 38.0 32 0.0007 28.0 2.8 29 150-178 68-96 (214)
175 TIGR01008 rpsC_E_A ribosomal p 37.9 33 0.00072 27.5 2.8 29 150-178 40-68 (195)
176 PLN00062 TATA-box-binding prot 37.4 2E+02 0.0044 22.6 8.6 25 45-69 54-80 (179)
177 PF02749 QRPTase_N: Quinolinat 37.0 1E+02 0.0022 21.0 4.8 54 166-220 32-85 (88)
178 PTZ00084 40S ribosomal protein 36.0 34 0.00073 28.0 2.6 30 150-179 46-75 (220)
179 TIGR01009 rpsC_bact ribosomal 34.3 34 0.00073 27.8 2.4 28 2-29 65-92 (211)
180 PRK03818 putative transporter; 33.9 3.3E+02 0.0072 25.6 9.1 123 87-216 217-360 (552)
181 COG0331 FabD (acyl-carrier-pro 33.7 67 0.0015 27.7 4.2 55 9-69 132-188 (310)
182 COG0331 FabD (acyl-carrier-pro 33.4 80 0.0017 27.2 4.6 68 157-231 131-203 (310)
183 PRK03818 putative transporter; 32.4 4.3E+02 0.0093 24.8 9.6 111 18-129 218-357 (552)
184 COG0490 Putative regulatory, l 31.1 60 0.0013 25.2 3.1 45 172-216 107-158 (162)
185 cd04517 TLF TBP-like factors ( 28.4 2.9E+02 0.0063 21.6 9.8 24 45-68 54-79 (174)
186 COG0490 Putative regulatory, l 27.7 1E+02 0.0022 23.9 3.9 44 23-66 107-158 (162)
187 cd04910 ACT_AK-Ectoine_1 ACT d 26.7 1.9E+02 0.0042 19.0 5.3 53 14-71 12-66 (71)
188 TIGR00119 acolac_sm acetolacta 26.3 3E+02 0.0066 21.1 8.1 89 114-218 46-140 (157)
189 TIGR03131 malonate_mdcH malona 25.4 99 0.0021 26.0 3.9 49 161-218 125-173 (295)
190 cd07049 BMC_EutL_repeat1 ethan 24.9 1.9E+02 0.0041 20.6 4.5 50 170-219 42-97 (103)
191 TIGR01009 rpsC_bact ribosomal 24.8 66 0.0014 26.1 2.5 28 150-177 64-91 (211)
192 PF00936 BMC: BMC domain; Int 24.4 2.2E+02 0.0047 18.7 4.9 27 196-222 39-65 (75)
193 PRK00310 rpsC 30S ribosomal pr 24.3 57 0.0012 26.9 2.1 28 2-29 65-92 (232)
194 PF02749 QRPTase_N: Quinolinat 24.0 2E+02 0.0043 19.5 4.5 50 19-68 34-83 (88)
195 cd07046 BMC_PduU-EutS 1,2-prop 23.1 1.1E+02 0.0023 22.1 3.1 32 197-232 74-105 (110)
196 cd07045 BMC_CcmK_like Carbon d 22.4 2.6E+02 0.0056 18.9 6.5 37 196-232 38-74 (84)
197 PF09383 NIL: NIL domain; Int 21.1 1.5E+02 0.0033 19.2 3.4 53 166-218 15-69 (76)
198 cd04518 TBP_archaea archaeal T 20.6 4.2E+02 0.0091 20.7 8.6 25 112-137 146-170 (174)
199 PF05651 Diacid_rec: Putative 20.3 2.8E+02 0.0061 20.6 5.0 95 21-137 10-109 (135)
No 1
>KOG1676|consensus
Probab=99.96 E-value=3.9e-28 Score=213.97 Aligned_cols=218 Identities=17% Similarity=0.252 Sum_probs=179.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc----------
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL---------- 71 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~---------- 71 (238)
++.||.+.+|.||||+|.+||.|++++||++.+-..+....+ ....+.|+|+++.|+.|+.++.+++.+
T Consensus 142 eI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~-~~KplritGdp~~ve~a~~lV~dil~e~~~~~~g~~~ 220 (600)
T KOG1676|consen 142 EILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG-ADKPLRITGDPDKVEQAKQLVADILREEDDEVPGSGG 220 (600)
T ss_pred eeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC-CCCceeecCCHHHHHHHHHHHHHHHHhcccCCCcccc
Confidence 578999999999999999999999999999999776654322 457999999999999999999888762
Q ss_pred ----------eEEEeecC--cCCCCCCCChHHHHHHHHhCceEEeeCC--CCCCCcEEEEEccccchHHHHHHHHHHHHH
Q psy11278 72 ----------IFCFEYPL--MGSTPNANSPFVQIIQEAYNVQVMFRNR--PKLQPTLVMVKGCEKDVERVKEATTKLIEH 137 (238)
Q Consensus 72 ----------~~~~~~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~--~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~ 137 (238)
.+.+++|. ++..+|++|++||+|+.++|++|+|.+. |.+..+.+.|.|.++.+.+|.+.|.+++..
T Consensus 221 ~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~ 300 (600)
T KOG1676|consen 221 HAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAE 300 (600)
T ss_pred ccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHH
Confidence 13344564 3447899999999999999999999764 344579999999999999999999998886
Q ss_pred hhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHH
Q psy11278 138 MCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYL 210 (238)
Q Consensus 138 ~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~ 210 (238)
..... .-..-....+.||+..++++||++|++||.|..+|||++.++... ++ ...+++.|+|+|++.+|.-
T Consensus 301 ~~~~~~~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~-p~-~~~~ektf~IrG~~~QIdh 378 (600)
T KOG1676|consen 301 AEAGAGGGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQP-PN-GNPKEKTFVIRGDKRQIDH 378 (600)
T ss_pred HhccCCCCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCCC-CC-CCccceEEEEecCcccchH
Confidence 54431 000101478999999999999999999999999999999887661 11 1225899999999999999
Q ss_pred HHHHHHhhcCCC
Q psy11278 211 ARQMLVVSSVRP 222 (238)
Q Consensus 211 A~~~I~~~l~~~ 222 (238)
|+.+|++.+..+
T Consensus 379 Ak~LIr~kvg~~ 390 (600)
T KOG1676|consen 379 AKQLIRDKVGDI 390 (600)
T ss_pred HHHHHHHHhccc
Confidence 999999999663
No 2
>KOG2193|consensus
Probab=99.94 E-value=6.2e-27 Score=198.32 Aligned_cols=230 Identities=17% Similarity=0.221 Sum_probs=180.0
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc-e----EEE
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL-I----FCF 75 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~-~----~~~ 75 (238)
|+++||..++|.||||.|+||+.|.+.|.++|++..... .+..++.++|.|.+|+..+|+++|.+++.. . +.-
T Consensus 201 lR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken--~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~k~~~ 278 (584)
T KOG2193|consen 201 LRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN--AGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDDKVAE 278 (584)
T ss_pred eeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc--CCcccCceEEecCccchHHHHHHHHHHHHHhhhccchhh
Confidence 689999999999999999999999999999999976443 244678999999999999999999887541 1 223
Q ss_pred eec--------CcCCCCCCCChHHHHHHHHhCceEEeeCCCCC----CCcEEEEEccccchHHHHHHHHHHHHHhhcc--
Q psy11278 76 EYP--------LMGSTPNANSPFVQIIQEAYNVQVMFRNRPKL----QPTLVMVKGCEKDVERVKEATTKLIEHMCGS-- 141 (238)
Q Consensus 76 ~~p--------~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~----~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~-- 141 (238)
++| +.+.++|+.|.++++|+.++|.+|.+.+..+. ..+.++++|.-+.|..|...|+.-+....++
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl 358 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDL 358 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhH
Confidence 344 24457899999999999999999998764222 3689999999888877776666555432211
Q ss_pred ----cc----------------cc--------------------------ceEEEEEEeCCCeeeEEecCCCchHHHHHH
Q psy11278 142 ----LA----------------NQ--------------------------TSVIMMMEISPQHHPIMEGPNAINLKTIMA 175 (238)
Q Consensus 142 ----~~----------------~~--------------------------~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~ 175 (238)
++ +. ......+.||...+|.|||++|.+|+.|.+
T Consensus 359 ~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~R 438 (584)
T KOG2193|consen 359 AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSR 438 (584)
T ss_pred HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHH
Confidence 00 00 012378899999999999999999999999
Q ss_pred HhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC--------CceEEEEeecCCc
Q psy11278 176 QTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP--------RRRLLLITIPNDI 235 (238)
Q Consensus 176 ~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~--------~p~~~~~~~~~~~ 235 (238)
.+||+|++..+.-++. .+++|+|+|++++..+|+.+|...++.- ..+...+.||...
T Consensus 439 fagASiKIappE~pdv---seRMViItGppeaqfKAQgrifgKikEenf~~PkeevklethirVPs~~ 503 (584)
T KOG2193|consen 439 FAGASIKIAPPEIPDV---SERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSA 503 (584)
T ss_pred hccceeeecCCCCCCc---ceeEEEecCChHHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchh
Confidence 9999999976665543 5899999999999999999999988542 3455666666543
No 3
>KOG1676|consensus
Probab=99.94 E-value=1.3e-25 Score=198.13 Aligned_cols=214 Identities=19% Similarity=0.290 Sum_probs=172.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce---------
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI--------- 72 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~--------- 72 (238)
+..||...++++|||+|+-|..|+.++||+++++...... ..|.+.+.|.+++|+.|+.+|.+.....
T Consensus 57 ~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~---~~r~~~~~G~pe~v~~aK~li~evv~r~~~~~~~~~~ 133 (600)
T KOG1676|consen 57 RYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGI---GYRSVDLTGSPENVEVAKQLIGEVVSRGRPPGGFPDN 133 (600)
T ss_pred ccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCc---ccccccccCCcccHHHHHHhhhhhhhccCCCCCcccc
Confidence 4579999999999999999999999999999987654322 4689999999999999999997763211
Q ss_pred -----EEEe--ecC--cCCCCCCCChHHHHHHHHhCceEEeeCCC---CCCCcEEEEEccccchHHHHHHHHHHHHHhhc
Q psy11278 73 -----FCFE--YPL--MGSTPNANSPFVQIIQEAYNVQVMFRNRP---KLQPTLVMVKGCEKDVERVKEATTKLIEHMCG 140 (238)
Q Consensus 73 -----~~~~--~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~~---~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~ 140 (238)
.+.+ +|. .+..++++|.+|++|++.+||++.+.... ....+.+.|+|+++.++.|+..+.++|.....
T Consensus 134 q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~ 213 (600)
T KOG1676|consen 134 QGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDD 213 (600)
T ss_pred CCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhccc
Confidence 2333 343 22367899999999999999998775431 11357899999999999999888888874322
Q ss_pred ccccc---------ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHH
Q psy11278 141 SLANQ---------TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211 (238)
Q Consensus 141 ~~~~~---------~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A 211 (238)
+.... -+.+.+|.||...||.||||+|++||+|+.+|||+|.|-.++++.. .+|.+.|.|+++.|+.|
T Consensus 214 ~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~s---peR~~~IiG~~d~ie~A 290 (600)
T KOG1676|consen 214 EVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSS---PERPAQIIGTVDQIEHA 290 (600)
T ss_pred CCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCC---ccceeeeecCHHHHHHH
Confidence 21100 1235899999999999999999999999999999999977666532 58999999999999999
Q ss_pred HHHHHhhcCC
Q psy11278 212 RQMLVVSSVR 221 (238)
Q Consensus 212 ~~~I~~~l~~ 221 (238)
.++|.+++.+
T Consensus 291 a~lI~eii~~ 300 (600)
T KOG1676|consen 291 AELINEIIAE 300 (600)
T ss_pred HHHHHHHHHH
Confidence 9999999943
No 4
>KOG2193|consensus
Probab=99.91 E-value=1.6e-24 Score=183.81 Aligned_cols=214 Identities=12% Similarity=0.197 Sum_probs=166.9
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce--------
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI-------- 72 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~-------- 72 (238)
|+++-...++|.+|||.|.+||+|+++||++|.|.+..+.+-.+.+|.|+|.|+.|+|.+|..+|++.+.++
T Consensus 282 Lk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~ 361 (584)
T KOG2193|consen 282 LKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAM 361 (584)
T ss_pred hhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHh
Confidence 345556778999999999999999999999999988776554556899999999999999999985432210
Q ss_pred ---------------------------------EEEee------------------cC--cCCCCCCCChHHHHHHHHhC
Q psy11278 73 ---------------------------------FCFEY------------------PL--MGSTPNANSPFVQIIQEAYN 99 (238)
Q Consensus 73 ---------------------------------~~~~~------------------p~--~~~~~~~~g~~i~~i~~~~g 99 (238)
++|.- |. ++..+|++|.+|+.|.++.|
T Consensus 362 s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~Rfag 441 (584)
T KOG2193|consen 362 SLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAG 441 (584)
T ss_pred hccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhcc
Confidence 01000 00 11134688999999999999
Q ss_pred ceEEeeCC--CCCCCcEEEEEccccchHHHHHHHHHHHHHhhccc----cccceEEEEEEeCCCeeeEEecCCCchHHHH
Q psy11278 100 VQVMFRNR--PKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSL----ANQTSVIMMMEISPQHHPIMEGPNAINLKTI 173 (238)
Q Consensus 100 v~I~~~~~--~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~----~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I 173 (238)
++|.+.++ |+...+.|+|.|+++..-+|+.-+ ..++.++. .+...+...+.+|+...|.+|||||.+++++
T Consensus 442 ASiKIappE~pdvseRMViItGppeaqfKAQgri---fgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnEL 518 (584)
T KOG2193|consen 442 ASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRI---FGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNEL 518 (584)
T ss_pred ceeeecCCCCCCcceeEEEecCChHHHHhhhhhh---hhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHH
Confidence 99998764 454568999999998776666333 22222221 1234466899999999999999999999999
Q ss_pred HHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 174 MAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 174 ~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
+.-|+|.+.+|.+..++ .++.-+|.|.|..-+...|++.|.+++
T Consensus 519 Qnlt~AeV~vPrdqtpd--End~vivriiGhfyatq~aQrki~~iv 562 (584)
T KOG2193|consen 519 QNLTSAEVVVPRDQTPD--ENDQVIVRIIGHFYATQNAQRKIAHIV 562 (584)
T ss_pred hccccceEEccccCCCC--ccceeeeeeechhhcchHHHHHHHHHH
Confidence 99999999999887664 346789999999999999999999988
No 5
>KOG2192|consensus
Probab=99.91 E-value=3e-23 Score=166.91 Aligned_cols=211 Identities=18% Similarity=0.247 Sum_probs=162.6
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEE----Ee
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFC----FE 76 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~----~~ 76 (238)
|++++.++-+|.||||+|+|||.|+.+++++|.+++++. .+++++|+.+.+.|-.-.+.|.--+.+-+. ++
T Consensus 50 ~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~-----peri~tisad~~ti~~ilk~iip~lee~f~~~~pce 124 (390)
T KOG2192|consen 50 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG-----PERILTISADIETIGEILKKIIPTLEEGFQLPSPCE 124 (390)
T ss_pred EEEEEecccccceeccccccHHHHhhhccceeeccCCCC-----CceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCchh
Confidence 578899999999999999999999999999999999876 579999999999887766655433322111 11
Q ss_pred ec------CcCCCCCCCChHHHHHHHHhCceEEeeC--CCCCCCcEEEEEccccchHHHHHHHHHHHHHhh--c------
Q psy11278 77 YP------LMGSTPNANSPFVQIIQEAYNVQVMFRN--RPKLQPTLVMVKGCEKDVERVKEATTKLIEHMC--G------ 140 (238)
Q Consensus 77 ~p------~~~~~~~~~g~~i~~i~~~~gv~I~~~~--~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~--~------ 140 (238)
+. ..+..++.+|+.|++|+++|.+++.+-. .|.++.+.+.+.|.+++|-...+.+..++...- +
T Consensus 125 ~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~ 204 (390)
T KOG2192|consen 125 LRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYD 204 (390)
T ss_pred hhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCC
Confidence 21 2334678899999999999999887654 366677888889998888666555555443210 0
Q ss_pred -ccc-------------------------------------------------------------------------c--
Q psy11278 141 -SLA-------------------------------------------------------------------------N-- 144 (238)
Q Consensus 141 -~~~-------------------------------------------------------------------------~-- 144 (238)
++. +
T Consensus 205 p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~Sew 284 (390)
T KOG2192|consen 205 PNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEW 284 (390)
T ss_pred ccccCcccccCCceeecCCCCCCCCCCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCcccc
Confidence 000 0
Q ss_pred ---------------c------------ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278 145 ---------------Q------------TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS 197 (238)
Q Consensus 145 ---------------~------------~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~ 197 (238)
. --.+++|+||+++-+.|||++|++|++|++++||.|++..+.+.. .++
T Consensus 285 qmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGs----edr 360 (390)
T KOG2192|consen 285 QMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGS----EDR 360 (390)
T ss_pred ccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCC----Cce
Confidence 0 023699999999999999999999999999999999997754432 369
Q ss_pred EEEEEcCHHHHHHHHHHHHhhcC
Q psy11278 198 SVTVSGNIDSVYLARQMLVVSSV 220 (238)
Q Consensus 198 ~v~I~G~~~~v~~A~~~I~~~l~ 220 (238)
.++|+|+.++++.|+.+++..+.
T Consensus 361 IitItGTqdQIqnAQYLlQn~Vk 383 (390)
T KOG2192|consen 361 IITITGTQDQIQNAQYLLQNSVK 383 (390)
T ss_pred EEEEeccHHHHhhHHHHHHHHHH
Confidence 99999999999999999998873
No 6
>KOG2191|consensus
Probab=99.86 E-value=1.4e-20 Score=155.58 Aligned_cols=164 Identities=20% Similarity=0.261 Sum_probs=127.6
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCc
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLM 80 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~ 80 (238)
|+|+||+...|.||||+|++|.+++++|||+|++++..+..|...+|++.|+|+.+++....+.|.+.+.
T Consensus 41 ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKir---------- 110 (402)
T KOG2191|consen 41 LKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIR---------- 110 (402)
T ss_pred EEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHH----------
Confidence 6899999999999999999999999999999999999999999999999999999999999888864422
Q ss_pred CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278 81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP 160 (238)
Q Consensus 81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~ 160 (238)
+.-...+-.+.+.+ |.. ++ .. -...+.+|....+
T Consensus 111 ------------e~p~~~~k~v~~~~-pqt----------~~------------------r~-----kqikivvPNstag 144 (402)
T KOG2191|consen 111 ------------EKPQAVAKPVDILQ-PQT----------PD------------------RI-----KQIKIVVPNSTAG 144 (402)
T ss_pred ------------HhHHhhcCCccccC-CCC----------cc------------------cc-----ceeEEeccCCccc
Confidence 11111111011100 000 00 00 0167788999999
Q ss_pred EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC
Q psy11278 161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR 221 (238)
Q Consensus 161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~ 221 (238)
.||||+|.+||.+++++||+|++.... +......++.+|+.|.+++..+|..+|.+.+..
T Consensus 145 ~iigkggAtiK~~~Eqsga~iqisPqk-pt~~sLqervvt~sge~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 145 MIIGKGGATIKAIQEQSGAWIQISPQK-PTGISLQERVVTVSGEPEQNMKAVSLILQKIQE 204 (402)
T ss_pred ceecCCcchHHHHHHhhCcceEecccC-CCCccceeEEEEecCCHHHHHHHHHHHHHHhhc
Confidence 999999999999999999999986322 222344689999999999999999999999844
No 7
>KOG2190|consensus
Probab=99.80 E-value=1.3e-18 Score=155.35 Aligned_cols=214 Identities=16% Similarity=0.231 Sum_probs=153.2
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce--------
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI-------- 72 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~-------- 72 (238)
++++||++++|.||||+|+.||+|+++|||+|.+.+... |...++.|+|.|.++.|.+|...|-.++-+.
T Consensus 140 ~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~l--P~ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~ 217 (485)
T KOG2190|consen 140 CRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDML--PNSTERAVTISGEPDAVKKALVQISSRLLENPPRSPPPL 217 (485)
T ss_pred EEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCC--CcccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCC
Confidence 479999999999999999999999999999999988643 4446788999999999999999884432110
Q ss_pred -EEEe-ec--------------------------------------C--cCCCCCCCChHHHHHHHHhCceEEeeCCCCC
Q psy11278 73 -FCFE-YP--------------------------------------L--MGSTPNANSPFVQIIQEAYNVQVMFRNRPKL 110 (238)
Q Consensus 73 -~~~~-~p--------------------------------------~--~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~ 110 (238)
.+.. .| . .+...++.+..++.++..++..+.+...-.
T Consensus 218 ~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~- 296 (485)
T KOG2190|consen 218 VSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRT- 296 (485)
T ss_pred CCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccC-
Confidence 0000 01 0 001235678889999999999988865311
Q ss_pred CCcEEEEEccc--c-chHHHHHHHHHHHHHhhccc-cc-cceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 111 QPTLVMVKGCE--K-DVERVKEATTKLIEHMCGSL-AN-QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 111 ~~~~v~I~G~~--~-~v~~a~~ai~~~~~~~~~~~-~~-~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
.+.+++.... + ....+++|+........+.. .+ ...++.++.+|+++++++||++|.+|.+|++.|||.|++-.
T Consensus 297 -~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~ 375 (485)
T KOG2190|consen 297 -DRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILN 375 (485)
T ss_pred -cceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCccccceeecccccchHHHHHhcCCceEEcc
Confidence 1455555443 1 11234445333222221111 11 33567999999999999999999999999999999999976
Q ss_pred CCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278 186 ANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV 220 (238)
Q Consensus 186 ~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~ 220 (238)
..+. ...++..++|+|...+...|+.++...+.
T Consensus 376 ~~~~--~~~~e~~~~I~~~~~~~~~~~~~~~~~~~ 408 (485)
T KOG2190|consen 376 KEEV--SGVREALVQITGMLREDLLAQYLIRARLS 408 (485)
T ss_pred cccc--CCcceeEEEecchhHHHHhhhhhcccccc
Confidence 5541 01257999999999999999999976663
No 8
>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=99.71 E-value=7.3e-17 Score=126.68 Aligned_cols=147 Identities=19% Similarity=0.298 Sum_probs=107.3
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEE---EeCHHHHHHHHHHHHhhCCceEEEeecC
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSI---AGSLLGLERARYRVRELTPLIFCFEYPL 79 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I---~G~~~~v~~A~~~I~~~~~~~~~~~~p~ 79 (238)
+.||.+.+|.|||++|++|+.|+++||++|++.+. +..|.| +++++++.+|++.|..+.... + |.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~--------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf---~-~e 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE--------TGEVKIEEEDEDPLAVMKAREVVKAIGRGF---S-PE 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC--------CceEEEecCCCCHHHHHHHHHHHHHHHcCC---C-HH
Confidence 57999999999999999999999999999999763 357888 689999999999998763321 1 00
Q ss_pred cCCCCCCCChHHHHHHHHhCceE-EeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCe
Q psy11278 80 MGSTPNANSPFVQIIQEAYNVQV-MFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQH 158 (238)
Q Consensus 80 ~~~~~~~~g~~i~~i~~~~gv~I-~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~ 158 (238)
.-.+-+.+.|...+ .+.+ + .+.+ .. + ...
T Consensus 70 ---------~A~~l~gd~y~~~Vi~I~~--------~--~~~~---~~--------~--------------------~~~ 99 (172)
T TIGR03665 70 ---------KALKLLDDDYMLEVIDLKE--------Y--GKSP---NA--------L--------------------RRI 99 (172)
T ss_pred ---------HHHHhcCCcceEEEEEhhh--------c--cCCH---HH--------H--------------------HHH
Confidence 00011222222221 1110 0 0110 00 0 014
Q ss_pred eeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278 159 HPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP 222 (238)
Q Consensus 159 ~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~ 222 (238)
.+.|||++|.+++.|+..|||+|.++. ..|.|.|++++++.|+..|++++...
T Consensus 100 ~griIG~~G~t~~~ie~~t~~~i~i~~-----------~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 100 KGRIIGEGGKTRRIIEELTGVSISVYG-----------KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred HhhhcCCCcHHHHHHHHHHCCeEEEcC-----------CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 688999999999999999999999974 47999999999999999999999654
No 9
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.68 E-value=4.2e-16 Score=123.17 Aligned_cols=147 Identities=19% Similarity=0.274 Sum_probs=108.2
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEE----eCHHHHHHHHHHHHhhCCceEEEee
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIA----GSLLGLERARYRVRELTPLIFCFEY 77 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~~~~~~~~~~ 77 (238)
.+.||.+.++.|||++|++|+.|+++||++|++.+. .+.|.|. ++++++.+|++.|..+.... +
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~--------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf---~- 73 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE--------TGEVIIEPTDGEDPLAVLKARDIVKAIGRGF---S- 73 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC--------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCC---C-
Confidence 588999999999999999999999999999999863 3688885 79999999999998874320 1
Q ss_pred cCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEE--ccccchHHHHHHHHHHHHHhhccccccceEEEEEEeC
Q psy11278 78 PLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVK--GCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEIS 155 (238)
Q Consensus 78 p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~--G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~ 155 (238)
|. ...+-+.+.|...+ +.|. +... .. .
T Consensus 74 ~e---------~A~~l~gd~y~~~V------------i~i~~~~~~~----------~~--------------------~ 102 (180)
T PRK13763 74 PE---------KALRLLDDDYVLEV------------IDLSDYGDSP----------NA--------------------L 102 (180)
T ss_pred HH---------HHHHHhCCCceEEE------------EEhhhccCCh----------hH--------------------H
Confidence 00 00111222221111 1110 0000 00 0
Q ss_pred CCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278 156 PQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP 222 (238)
Q Consensus 156 ~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~ 222 (238)
...+|.|||++|.+++.|++.|||+|.++. ..|.|.|+++++..|+..|..++...
T Consensus 103 ~r~~griIG~~G~~~k~ie~~t~~~i~i~~-----------~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 103 RRIKGRIIGEGGKTRRIIEELTGVDISVYG-----------KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHHhhheeCCCcHHHHHHHHHHCcEEEEcC-----------CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 125799999999999999999999999963 34999999999999999999999654
No 10
>KOG2190|consensus
Probab=99.68 E-value=5e-16 Score=138.82 Aligned_cols=156 Identities=21% Similarity=0.173 Sum_probs=119.2
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe---------CHHHHHHHHHHHHhhCCc
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG---------SLLGLERARYRVRELTPL 71 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G---------~~~~v~~A~~~I~~~~~~ 71 (238)
.+++.+.+++|.||||+|..+++|+.+|+++|++.+... ++.+|+++|+| ..+++.+|..+|-....+
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~---~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLP---GCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCC---CCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence 378999999999999999999999999999999987643 33679999999 677777777776321110
Q ss_pred eEEEeecCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEE
Q psy11278 72 IFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMM 151 (238)
Q Consensus 72 ~~~~~~p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~ 151 (238)
. - ....+. | ...+.-.++..
T Consensus 122 d-------------------------~---~~~~d~-----------~---------------------~~~~~~~v~~R 141 (485)
T KOG2190|consen 122 D-------------------------D---EAAEDN-----------G---------------------EDASGPEVTCR 141 (485)
T ss_pred c-------------------------c---cccccC-----------C---------------------ccccCCceEEE
Confidence 0 0 000000 0 00000025589
Q ss_pred EEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRP 222 (238)
Q Consensus 152 v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~ 222 (238)
+.||..++|.||||+|+.|++|+++|||+|.+-.+..|.+ .++.|+|.|.+++|.+|...|...|-..
T Consensus 142 LlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~s---ter~V~IsG~~~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 142 LLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNS---TERAVTISGEPDAVKKALVQISSRLLEN 209 (485)
T ss_pred EEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcc---cceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999877655554 4788999999999999999999998553
No 11
>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=99.51 E-value=3.2e-14 Score=93.01 Aligned_cols=59 Identities=36% Similarity=0.685 Sum_probs=54.9
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV 65 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I 65 (238)
++.||.++|+.|||++|++|++|+++|||+|++++.+. .++.|+|+|++++|..|+.+|
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~-----~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGS-----KSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCC-----CCCEEEEEcCHHHHHHHHHHh
Confidence 68999999999999999999999999999999998653 568999999999999999987
No 12
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.50 E-value=6.9e-14 Score=92.29 Aligned_cols=63 Identities=30% Similarity=0.471 Sum_probs=56.7
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV 65 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I 65 (238)
+++.||.+.+|.|||++|++|++|+++|||+|++++..+ +...++.|+|+|+++++..|+.+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~--~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL--PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC--CCCCceEEEEEeCHHHHHHHHHhh
Confidence 479999999999999999999999999999999987654 233678999999999999999987
No 13
>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=99.49 E-value=5.3e-14 Score=92.00 Aligned_cols=61 Identities=26% Similarity=0.512 Sum_probs=55.9
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 216 (238)
..+.||..+|++|||++|++|++|+++|||+|.+|+..++ .+.|+|+|++++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~------~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSK------SDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCC------CCEEEEEcCHHHHHHHHHHhC
Confidence 5789999999999999999999999999999999987643 589999999999999998874
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=99.44 E-value=4.2e-13 Score=88.52 Aligned_cols=63 Identities=22% Similarity=0.275 Sum_probs=56.3
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHH
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I 215 (238)
.++.||...+++|||++|.+|++|+++|||+|.+++..+++ ..++.|+|.|+++++..|+.+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~---~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPG---STERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCC---CCceEEEEEeCHHHHHHHHHhh
Confidence 67899999999999999999999999999999998765421 1478999999999999999987
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=99.42 E-value=1e-13 Score=90.04 Aligned_cols=60 Identities=27% Similarity=0.429 Sum_probs=55.0
Q ss_pred EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHH
Q psy11278 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215 (238)
Q Consensus 149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I 215 (238)
|.+|.||..++++|||++|++|++|+++|||.|.||+.+ +...|+|+|++++|..|+++|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD-------ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT-------EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC-------CcEEEEEEeCHHHHHHHHhhC
Confidence 478999999999999999999999999999999998762 257999999999999999886
No 16
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.42 E-value=6.5e-13 Score=86.34 Aligned_cols=55 Identities=35% Similarity=0.527 Sum_probs=51.2
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-HHHHHHHHHHH
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRV 65 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I 65 (238)
.+.||.+.++.|||++|++|++|+++|||+|++++ ++.|.|+|+ +++++.|+.+|
T Consensus 5 ~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 5 TMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---------CCEEEEEeCCHHHHHHHHHHh
Confidence 57899999999999999999999999999999986 258999998 99999999987
No 17
>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=99.39 E-value=1.9e-13 Score=88.73 Aligned_cols=59 Identities=32% Similarity=0.560 Sum_probs=53.3
Q ss_pred CEEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV 65 (238)
Q Consensus 1 ~~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I 65 (238)
.+|.||.++++.|||++|++|++|+++|||+|++++.+ ....|+|+|++++|+.|+++|
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~------~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDD------ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTT------EEEEEEEEESHHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCC------CcEEEEEEeCHHHHHHHHhhC
Confidence 37899999999999999999999999999999998751 235999999999999999886
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=99.37 E-value=2.9e-12 Score=83.29 Aligned_cols=58 Identities=24% Similarity=0.419 Sum_probs=53.0
Q ss_pred EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHH
Q psy11278 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLV 216 (238)
Q Consensus 149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~ 216 (238)
...+.||+.++++|||++|++|++|+++|||+|.+++. ..|+|+|+ +++++.|+.+|+
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~----------g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD----------GTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCCC----------CEEEEEeCCHHHHHHHHHHhC
Confidence 36889999999999999999999999999999999862 47999998 999999998874
No 19
>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=99.36 E-value=3.1e-12 Score=83.97 Aligned_cols=63 Identities=21% Similarity=0.339 Sum_probs=56.1
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 216 (238)
.++.||..++++|||++|++|++|+++|||.|.++...+.. ..+.|+|.|+.+++..|+.+|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~----~~~~v~i~G~~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGS----EERIVTITGTPEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCC----CceEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999765321 4689999999999999998874
No 20
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.35 E-value=4.1e-12 Score=83.35 Aligned_cols=61 Identities=34% Similarity=0.554 Sum_probs=54.7
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHH
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV 65 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I 65 (238)
++.||.++++.|||++|++|++|+++|||+|.++.... ...++.|.|.|+.+++..|+.+|
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~---~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS---GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC---CCCceEEEEEcCHHHHHHHHHHh
Confidence 68999999999999999999999999999999988543 12467999999999999999886
No 21
>KOG2192|consensus
Probab=99.28 E-value=1.8e-11 Score=99.28 Aligned_cols=133 Identities=11% Similarity=0.134 Sum_probs=104.9
Q ss_pred CCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeee
Q psy11278 81 GSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHP 160 (238)
Q Consensus 81 ~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~ 160 (238)
+..++++|.+|+.|+.+|++++++++.. ...+.++|+.+.+.+-. -++.++..+.+.++-.....+.+.|..++.+
T Consensus 60 gavigkgg~nik~lr~d~na~v~vpds~-~peri~tisad~~ti~~---ilk~iip~lee~f~~~~pce~rllihqs~ag 135 (390)
T KOG2192|consen 60 GAVIGKGGKNIKALRTDYNASVSVPDSS-GPERILTISADIETIGE---ILKKIIPTLEEGFQLPSPCELRLLIHQSLAG 135 (390)
T ss_pred cceeccccccHHHHhhhccceeeccCCC-CCceeEEEeccHHHHHH---HHHHHhhhhhhCCCCCCchhhhhhhhhhhcc
Confidence 3367899999999999999999998742 23578999988554433 4455555554444333334478899999999
Q ss_pred EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278 161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV 220 (238)
Q Consensus 161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~ 220 (238)
.|||++|++|+++++++.|++++-....|++ ..+++.+.|.+..|-.+.+.|++++.
T Consensus 136 ~iigrngskikelrekcsarlkift~c~p~s---tdrv~l~~g~~k~v~~~i~~il~~i~ 192 (390)
T KOG2192|consen 136 GIIGRNGSKIKELREKCSARLKIFTECCPHS---TDRVVLIGGKPKRVVECIKIILDLIS 192 (390)
T ss_pred ceecccchhHHHHHHhhhhhhhhhhccCCCC---cceEEEecCCcchHHHHHHHHHHHhh
Confidence 9999999999999999999998877666654 46888899999999999999999983
No 22
>PF13014 KH_3: KH domain
Probab=99.16 E-value=6e-11 Score=71.52 Aligned_cols=43 Identities=40% Similarity=0.659 Sum_probs=36.6
Q ss_pred ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe
Q psy11278 9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG 53 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G 53 (238)
+||+|||++|++|++|+++|+|+|+|++... +...++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~--~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENE--PGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccC--CCCCceEEEEEC
Confidence 5899999999999999999999999999222 334678999987
No 23
>KOG2208|consensus
Probab=99.14 E-value=1.3e-10 Score=109.80 Aligned_cols=202 Identities=20% Similarity=0.278 Sum_probs=148.7
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce------EEE
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI------FCF 75 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~------~~~ 75 (238)
.+.|-+.++..++||+|+++.+||++++|.|.++.... ....++++|...++.+|.+.+.....+. ..+
T Consensus 350 ~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~-----~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~~~~~~~ 424 (753)
T KOG2208|consen 350 KREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGS-----NNKKVVITGVSANDEKAVEDVEKIIAEILNSIVKEEV 424 (753)
T ss_pred EEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccC-----CCCCeEEeccccchhHHHHHHHHHHHhhhccccccee
Confidence 35677888999999999999999999999999998543 4579999999999999999987765433 336
Q ss_pred eecCcC--CCCCCCChHHHHHHHHhC-ceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEE
Q psy11278 76 EYPLMG--STPNANSPFVQIIQEAYN-VQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMM 152 (238)
Q Consensus 76 ~~p~~~--~~~~~~g~~i~~i~~~~g-v~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v 152 (238)
.+|... ...+.+|..|..|+.+++ +.+.++.. .......+++|....+..++..+..+... ..+. .+...+
T Consensus 425 ~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~-~~~~~~~~~~~~~~dv~~~~~~~~~~~~~-a~~~----~~~~~~ 498 (753)
T KOG2208|consen 425 QIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN-NNSSDMVTIRGISKDVEKSVSLLKALKAD-AKNL----KFRDVV 498 (753)
T ss_pred ecCccchhhhhccccccHHHHHhhcCcEEEecCCC-CcccccceEeccccccchhHHHHHhhhhh-hhcc----hhhhhh
Confidence 667533 366788999999999998 88888753 33456788888888887755443332221 1111 111222
Q ss_pred EeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 153 EISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 153 ~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
.=...++...+|+.+.....++...+....||...+. +...++|.|..+.|.+|+..|..+.
T Consensus 499 ~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~~-----~~~~i~i~gk~~~v~~a~~~L~~~~ 560 (753)
T KOG2208|consen 499 TKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNEDE-----DHEKITIEGKLELVLEAPAELKALI 560 (753)
T ss_pred hccccchHHhhcccccCceeeeccCCceeeccccccc-----ccceeeecccccchhhhHHHHHhcc
Confidence 2333455666666666677778888888888876433 3689999999999999999999887
No 24
>KOG2208|consensus
Probab=99.13 E-value=2.5e-10 Score=107.78 Aligned_cols=218 Identities=23% Similarity=0.306 Sum_probs=143.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCC--CCeEEEEeCHHHHHHHHHHHHh--hCCceEEEee
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEK--SNQVSIAGSLLGLERARYRVRE--LTPLIFCFEY 77 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~--~~~v~I~G~~~~v~~A~~~I~~--~~~~~~~~~~ 77 (238)
++.+-...|+++||++|.++..+++++.+++++|..+...+... .+...+......+..|..+++. ..+......+
T Consensus 204 k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~~~~~ 283 (753)
T KOG2208|consen 204 KMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEIIYRRL 283 (753)
T ss_pred EeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhhhccc
Confidence 56778889999999999999999999999999998876432211 1223333333344444444422 1111111111
Q ss_pred cCcCCCCCCCChHHHHHHHHh-CceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCC
Q psy11278 78 PLMGSTPNANSPFVQIIQEAY-NVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISP 156 (238)
Q Consensus 78 p~~~~~~~~~g~~i~~i~~~~-gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~ 156 (238)
|.. ..+..+..+..++..+ .+.+.++..| +....+.++|....+..+......++.....+ ++...+.+.+
T Consensus 284 ~~~--~~~~~~~~~~~~~~~~~~~~~i~~~~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n-----n~~i~~~i~~ 355 (753)
T KOG2208|consen 284 PRF--IRGIPGEEINQLRDYMPEVDSIFQNYP-SKDDSIVLSGFEVGAVLAKRDKTLLLKNSEEN-----NENIKREIFP 355 (753)
T ss_pred ccc--ccccccchhhHHHhhcchhhhhhcccc-ccceeEeecccccchhhhhhHHHHHHHHhhcc-----ceeeEEeecH
Confidence 111 2234466677776554 4444444422 33578899999877766554433333322222 1448899999
Q ss_pred CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC-CC-ceEEEEeecC
Q psy11278 157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR-PR-RRLLLITIPN 233 (238)
Q Consensus 157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~-~~-p~~~~~~~~~ 233 (238)
.++.+++|++|.++.+|++++.|.+.++...+. ...++++|...++.+|...++..... .+ ++.-.|-+|.
T Consensus 356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~------~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~~~~~~~~iP~ 428 (753)
T KOG2208|consen 356 EELKFVIGKKGANIEKIREESQVKIDLPKQGSN------NKKVVITGVSANDEKAVEDVEKIIAEILNSIVKEEVQIPT 428 (753)
T ss_pred HhhhhhcCCCCccHHHHHHhhhhceecccccCC------CCCeEEeccccchhHHHHHHHHHHHhhhcccccceeecCc
Confidence 999999999999999999999999999996554 47899999999999999998887744 33 3444455554
No 25
>smart00322 KH K homology RNA-binding domain.
Probab=99.13 E-value=2.9e-10 Score=74.92 Aligned_cols=63 Identities=32% Similarity=0.497 Sum_probs=56.5
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT 69 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~ 69 (238)
++.||.+.++.+||++|++|++|+++||++|.++.... ....+.|.|+.+++..|...|.+.+
T Consensus 6 ~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~-----~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 6 EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS-----EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred EEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC-----CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 68899999999999999999999999999999987542 3479999999999999999998753
No 26
>smart00322 KH K homology RNA-binding domain.
Probab=99.11 E-value=5.9e-10 Score=73.44 Aligned_cols=66 Identities=21% Similarity=0.330 Sum_probs=59.3
Q ss_pred EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
.+..+.||..+++++||++|++|++|++.+|++|.++..... ...++|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~------~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSE------ERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCC------ccEEEEEcCHHHHHHHHHHHHHHh
Confidence 347899999999999999999999999999999999875532 478999999999999999999876
No 27
>PF13014 KH_3: KH domain
Probab=99.10 E-value=1.9e-10 Score=69.32 Aligned_cols=43 Identities=30% Similarity=0.452 Sum_probs=36.4
Q ss_pred eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc
Q psy11278 158 HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG 203 (238)
Q Consensus 158 ~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G 203 (238)
+|++|||++|++|++|+++|||+|.||+...++ ..++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~---~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPG---SNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCC---CCceEEEEEC
Confidence 589999999999999999999999999932221 2579999998
No 28
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.99 E-value=2.3e-08 Score=78.37 Aligned_cols=152 Identities=16% Similarity=0.232 Sum_probs=107.5
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-----CHHHHHHHHHHHHhhCCceEEEe
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-----SLLGLERARYRVRELTPLIFCFE 76 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-----~~~~v~~A~~~I~~~~~~~~~~~ 76 (238)
.+.||....+.+||+.|..-+.|++.+++++.+... +..|+|.. +|..+.+|++.++.+-.- |+
T Consensus 11 ~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~--------~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG---F~ 79 (194)
T COG1094 11 AVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK--------TGSVTIRTTRKTEDPLALLKARDVVKAIGRG---FP 79 (194)
T ss_pred eeecCchhheeeecccccchHHHHhhcCeEEEEECC--------CCeEEEEecCCCCChHHHHHHHHHHHHHhcC---CC
Confidence 378999999999999999999999999999999773 45777753 688999999999866221 00
Q ss_pred ecCcCCCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCC
Q psy11278 77 YPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISP 156 (238)
Q Consensus 77 ~p~~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~ 156 (238)
. ..-++=++ + +..+.+-+ | .++.. ...+ .+ .
T Consensus 80 p----------e~A~~LL~-d-~~~levId----------i--------------~~~~~----~~~~--~l-------~ 110 (194)
T COG1094 80 P----------EKALKLLE-D-DYYLEVID----------L--------------KDVVT----LSGD--HL-------R 110 (194)
T ss_pred H----------HHHHHHhc-C-CcEEEEEE----------H--------------HHhcc----Cchh--hh-------h
Confidence 0 01122222 2 32222211 0 00000 0000 00 1
Q ss_pred CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCc
Q psy11278 157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRR 224 (238)
Q Consensus 157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p 224 (238)
...|.|||++|.+-+-|++-|||.|.+-. ..|-|.|.+++|..|++.|+.++.+..|
T Consensus 111 R~kgRIIG~~GkTr~~IE~lt~~~I~V~g-----------~tVaiiG~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 111 RIKGRIIGREGKTRRAIEELTGVYISVYG-----------KTVAIIGGFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred HhhceeeCCCchHHHHHHHHhCCeEEEeC-----------cEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence 24588999999999999999999999853 6799999999999999999999976543
No 29
>KOG2191|consensus
Probab=98.76 E-value=1.8e-08 Score=84.28 Aligned_cols=69 Identities=22% Similarity=0.301 Sum_probs=58.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP 70 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~ 70 (238)
++.+|.+-.|.||||+|++||.+++++++.|+|+......-.-.+|+|+++|++++..+|..+|.+.+.
T Consensus 135 kivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~ 203 (402)
T KOG2191|consen 135 KIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQNMKAVSLILQKIQ 203 (402)
T ss_pred EEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHHHHHHHHHHHHhh
Confidence 688999999999999999999999999999999743322122367899999999999999999976544
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=98.73 E-value=5.5e-08 Score=71.61 Aligned_cols=70 Identities=21% Similarity=0.241 Sum_probs=54.4
Q ss_pred EEEecC------CccceeeccCCccHHHHHHHcCCEEEecCCCCCC--------------CCCCCCeEEEEeC---HHHH
Q psy11278 2 KLDVSY------TDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSV--------------NAEKSNQVSIAGS---LLGL 58 (238)
Q Consensus 2 ~i~ip~------~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~--------------~~~~~~~v~I~G~---~~~v 58 (238)
++.||. +++|.|||++|+++|+|+++|||+|.|....... ..++...|.|+++ .+++
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~ 82 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEAL 82 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHH
Confidence 456665 3569999999999999999999999998763211 0123468999995 5999
Q ss_pred HHHHHHHHhhCCc
Q psy11278 59 ERARYRVRELTPL 71 (238)
Q Consensus 59 ~~A~~~I~~~~~~ 71 (238)
.+|+.+|..++..
T Consensus 83 ~~A~~~I~~ll~~ 95 (120)
T cd02395 83 AKAVEAIEELLKP 95 (120)
T ss_pred HHHHHHHHHHhcc
Confidence 9999999988653
No 31
>KOG2279|consensus
Probab=98.61 E-value=9.4e-08 Score=84.90 Aligned_cols=213 Identities=15% Similarity=0.175 Sum_probs=144.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCce--EEEeecC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI--FCFEYPL 79 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~--~~~~~p~ 79 (238)
++-+|...+..++||+|++|+.|+..|+++|.+...+.. +++.-++.|-+..+..|+..+.+..-.. +...++.
T Consensus 71 e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g----~e~~~~~~~~p~~v~~a~a~~~~~~~~~~pvk~~lsv 146 (608)
T KOG2279|consen 71 EMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG----DERVLLISGFPVQVCKAKAAIHQILTENTPVSEQLSV 146 (608)
T ss_pred eEeecccceeeeeccccCCcchhhcccccceecCcccCC----cccchhhccCCCCCChHHHHHHHHHhcCCcccccccc
Confidence 567899999999999999999999999999999776542 4567777778899999988886654322 2223322
Q ss_pred ----cCCCCCCCChHHHHHHHHhCceEEeeCCCCCC-CcEEEEEccccchHHHHHHHHHHHH-------Hhhcc------
Q psy11278 80 ----MGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQ-PTLVMVKGCEKDVERVKEATTKLIE-------HMCGS------ 141 (238)
Q Consensus 80 ----~~~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~-~~~v~I~G~~~~v~~a~~ai~~~~~-------~~~~~------ 141 (238)
.+..++.+|..++.+.+-.+++|.+....... .+...|.|..+-.+.++..+.+-++ ...+.
T Consensus 147 pqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvp 226 (608)
T KOG2279|consen 147 PQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVP 226 (608)
T ss_pred hhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCC
Confidence 22356778888888888888888776542222 2455555555544454432211111 00000
Q ss_pred cc-----------------------------------------c----------------------cceEEEEEEeCCCe
Q psy11278 142 LA-----------------------------------------N----------------------QTSVIMMMEISPQH 158 (238)
Q Consensus 142 ~~-----------------------------------------~----------------------~~~~~~~v~i~~~~ 158 (238)
++ + ......+|.+|.-.
T Consensus 227 rk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~l 306 (608)
T KOG2279|consen 227 RKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEIL 306 (608)
T ss_pred CCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCccc
Confidence 00 0 00112789999999
Q ss_pred eeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 159 HPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 159 ~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
++.+||+.|..+..+...+|+.++|-....... .....++.+.|+-.-+..|..++....
T Consensus 307 sg~lig~~gey~s~yssasn~~~hi~t~pyt~~-v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 307 SGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR-VLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred ccchhhhhhhhhhhhhhccCccceEEeccccch-hhhhhhheecchhHHHHHHHhhhhccC
Confidence 999999999999999999999987754332110 012267899999999999999988655
No 32
>KOG2113|consensus
Probab=98.59 E-value=4.3e-08 Score=81.44 Aligned_cols=151 Identities=19% Similarity=0.211 Sum_probs=107.9
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeecCcC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFCFEYPLMG 81 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~~ 81 (238)
.+.+|...++.+.|++|.+|+.++.+|+++|.-|... .+.+..++|..++|+.|+.+|..-.. -|.++.
T Consensus 29 sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~------eePiF~vTg~~edv~~aRrei~saae---H~~l~~-- 97 (394)
T KOG2113|consen 29 SVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG------EEPIFPVTGRHEDVRRARREIPSAAE---HFGLIR-- 97 (394)
T ss_pred eeecCcccceeecccCccccchhhhhhcceeccCCCC------CCCcceeccCchhHHHHhhcCccccc---eeeeee--
Confidence 4678988889999999999999999999999998865 35799999999999999998843211 111110
Q ss_pred CCCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeE
Q psy11278 82 STPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPI 161 (238)
Q Consensus 82 ~~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~ 161 (238)
......|..+... . . .+ .+.++.+|-..++.
T Consensus 98 -----------~s~s~Sgg~~~~s-----------~-----------------------s--~q--t~sy~svP~rvvgl 128 (394)
T KOG2113|consen 98 -----------ASRSFSGGTNGAS-----------A-----------------------S--GQ--TTSYVSVPLRVVGL 128 (394)
T ss_pred -----------ecccccCCCcccc-----------c-----------------------c--CC--Cceeeeccceeeee
Confidence 0010111000000 0 0 11 12567778889999
Q ss_pred EecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHH-HHHHH-HHHHhhc
Q psy11278 162 MEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDS-VYLAR-QMLVVSS 219 (238)
Q Consensus 162 iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~-v~~A~-~~I~~~l 219 (238)
+.|.+|.+|+.|++.++..|.-|-... +.++-++|-+.+ +++|+ ..|+.-.
T Consensus 129 vv~~~~~ti~~iqq~tnt~I~T~v~~~-------~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 129 VVGPKGATIKRIQQFTNTYIATPVRCG-------EPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred ccccccCccchheecccceEeeeccCC-------CceEEEecCCcchhhhccccchhhhh
Confidence 999999999999999999998876552 579999998888 66676 4454433
No 33
>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=98.46 E-value=2.5e-07 Score=72.68 Aligned_cols=52 Identities=29% Similarity=0.344 Sum_probs=48.2
Q ss_pred ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCC
Q psy11278 9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTP 70 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~ 70 (238)
..|.|||++|.+++.|+..|||+|.+++ ..|.|.|++++++.|+..|.++..
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~----------~~v~i~G~~~~~~~A~~~i~~li~ 150 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYG----------KTVGIIGDPEQVQIAREAIEMLIE 150 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcC----------CEEEEECCHHHHHHHHHHHHHHHc
Confidence 5799999999999999999999999975 589999999999999999998854
No 34
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.41 E-value=4.7e-07 Score=71.69 Aligned_cols=63 Identities=16% Similarity=0.218 Sum_probs=56.5
Q ss_pred EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEE----cCHHHHHHHHHHHHhhcC
Q psy11278 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVS----GNIDSVYLARQMLVVSSV 220 (238)
Q Consensus 149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~----G~~~~v~~A~~~I~~~l~ 220 (238)
...+.||++.++.|||++|++|+.|+++|||+|.+... ...|.|. ++++++.+|+.+|.++..
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~---------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE---------TGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC---------CCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 47899999999999999999999999999999999763 2567885 899999999999999884
No 35
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.36 E-value=2e-06 Score=63.38 Aligned_cols=65 Identities=15% Similarity=0.132 Sum_probs=51.0
Q ss_pred CeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCC-------------CCCcceEEEEEcC---HHHHHHHHHHHHhhcC
Q psy11278 157 QHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPII-------------PVLKKSSVTVSGN---IDSVYLARQMLVVSSV 220 (238)
Q Consensus 157 ~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~-------------~~~~~~~v~I~G~---~~~v~~A~~~I~~~l~ 220 (238)
+++|.|||.+|+++|+|+++|||+|.+-...+... ...+.--|.|+++ .+++.+|..+|+.++.
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 58899999999999999999999999976521100 0012367899996 5999999999999995
Q ss_pred C
Q psy11278 221 R 221 (238)
Q Consensus 221 ~ 221 (238)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 3
No 36
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.15 E-value=4.5e-06 Score=78.09 Aligned_cols=60 Identities=22% Similarity=0.361 Sum_probs=54.8
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP 70 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~ 70 (238)
.+.||.+.++.|||+||++||.|.++|||+|++.+ +..|.|.+ +.+.+++|+.+|..+..
T Consensus 581 ~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 581 TVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred EEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 57899999999999999999999999999999976 36899988 68999999999998865
No 37
>KOG2814|consensus
Probab=97.90 E-value=1.2e-05 Score=67.75 Aligned_cols=64 Identities=28% Similarity=0.338 Sum_probs=54.9
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCCc
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTPL 71 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~ 71 (238)
+.+++++.++|||++|.|.++|+++|+++|-+|.++. ....|+|.| ....|.+|..+|..++..
T Consensus 61 i~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~-----n~~~i~i~~~~~~~V~~a~~Ri~~~ids 125 (345)
T KOG2814|consen 61 ILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT-----NKEEIKIIGISRNCVIQALERIAKLIDS 125 (345)
T ss_pred hhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC-----CcceEEEeehhHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999999999999999875 345677766 778999999999776543
No 38
>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=97.89 E-value=6.2e-05 Score=70.67 Aligned_cols=87 Identities=18% Similarity=0.292 Sum_probs=67.9
Q ss_pred hHHHHHHHHHHHHHhhcc------ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278 124 VERVKEATTKLIEHMCGS------LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS 197 (238)
Q Consensus 124 v~~a~~ai~~~~~~~~~~------~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~ 197 (238)
.+.|+++...+++.+.+. +....+....+.||++..+.+||.||.+||+|.++|||.|.+.+ ..
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d----------~G 617 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTPDEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED----------DG 617 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCccccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------Cc
Confidence 345555555566554332 22223455889999999999999999999999999999999875 25
Q ss_pred EEEEEcC-HHHHHHHHHHHHhhcC
Q psy11278 198 SVTVSGN-IDSVYLARQMLVVSSV 220 (238)
Q Consensus 198 ~v~I~G~-~~~v~~A~~~I~~~l~ 220 (238)
.|.|.+. .++.++|+.+|+.+..
T Consensus 618 ~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 618 TVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred EEEEEeCCHHHHHHHHHHHHHhhC
Confidence 7999985 8999999999999985
No 39
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.88 E-value=1.7e-05 Score=75.03 Aligned_cols=60 Identities=27% Similarity=0.416 Sum_probs=53.2
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP 70 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~ 70 (238)
++.||.+.++.|||++|++||.|+++|||+|++.+ +..|.|.+ +.+.+++|+..|..+..
T Consensus 554 ~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---------dG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 554 TIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---------DGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred EEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 57899999999999999999999999999999975 35788876 68999999999987743
No 40
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.68 E-value=0.00013 Score=69.15 Aligned_cols=86 Identities=21% Similarity=0.308 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHHHhhcc-------ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278 125 ERVKEATTKLIEHMCGS-------LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS 197 (238)
Q Consensus 125 ~~a~~ai~~~~~~~~~~-------~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~ 197 (238)
..|+++...+++.+.+. +....+....+.||+...+.|||++|++|++|.++|||.|.+.++ .
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd----------G 590 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD----------G 590 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC----------e
Confidence 44455555555544322 222234557899999999999999999999999999999998652 4
Q ss_pred EEEEEc-CHHHHHHHHHHHHhhcC
Q psy11278 198 SVTVSG-NIDSVYLARQMLVVSSV 220 (238)
Q Consensus 198 ~v~I~G-~~~~v~~A~~~I~~~l~ 220 (238)
.|.|.+ ..+.+++|+++|..+..
T Consensus 591 ~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 591 TVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred EEEEEECcHHHHHHHHHHHHhhhc
Confidence 677777 58899999999998874
No 41
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.60 E-value=0.00015 Score=57.18 Aligned_cols=53 Identities=32% Similarity=0.331 Sum_probs=48.2
Q ss_pred ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278 9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL 71 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~ 71 (238)
..|.|||++|.+-+.|++-|+|.|.+.. ..|.|-|.+++|..|++.|..+...
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g----------~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYG----------KTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeC----------cEEEEecChhhhHHHHHHHHHHHcC
Confidence 3589999999999999999999999976 5999999999999999999888553
No 42
>KOG0119|consensus
Probab=97.53 E-value=0.00016 Score=64.02 Aligned_cols=64 Identities=19% Similarity=0.206 Sum_probs=49.9
Q ss_pred CccceeeccCCccHHHHHHHcCCEEEecCCCCC----------C---CCCCCCeEEEEe-CHHHHHHHHHHHHhhCCc
Q psy11278 8 TDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRS----------V---NAEKSNQVSIAG-SLLGLERARYRVRELTPL 71 (238)
Q Consensus 8 ~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~----------~---~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~ 71 (238)
+++|+|||..|.|.|+|+++|||+|.|-..... . ...++-.+.|++ +.+.|.+|...|+.++..
T Consensus 153 NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 153 NFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred ceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 578999999999999999999999999762211 0 112334788888 568999999999887654
No 43
>KOG2279|consensus
Probab=97.51 E-value=9e-05 Score=66.37 Aligned_cols=126 Identities=12% Similarity=0.205 Sum_probs=95.1
Q ss_pred CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeEE
Q psy11278 83 TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIM 162 (238)
Q Consensus 83 ~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~i 162 (238)
..+..|++++.+...+++++.+.+..-.......+.|.+..+.+++.++...+.. + ..+..+..+|...++.|
T Consensus 82 i~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~---~----~pvk~~lsvpqr~~~~i 154 (608)
T KOG2279|consen 82 IIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTE---N----TPVSEQLSVPQRSVGRI 154 (608)
T ss_pred eeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhc---C----Ccccccccchhhhcccc
Confidence 4456789999999999999998764222234455566888888888665544331 1 23557888899999999
Q ss_pred ecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 163 EGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 163 IG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
+|++|.+++.|+..++|+|.+....-. +..+...|.|...-+..|+.++.+.+
T Consensus 155 ~grgget~~si~~ss~aki~~d~ngr~----g~~~~~~i~~qqk~~~~a~~~~~~~~ 207 (608)
T KOG2279|consen 155 IGRGGETIRSICKSSGAKITCDKNGRL----GLSRLIKISGQQKEVAAAKHLILEKV 207 (608)
T ss_pred cccchhhhcchhccccccccccccccc----ccccceecccccchHHHHHhhhhccc
Confidence 999999999999999999998765422 23567777777777778998888776
No 44
>KOG2113|consensus
Probab=97.45 E-value=0.0001 Score=61.69 Aligned_cols=63 Identities=22% Similarity=0.320 Sum_probs=57.6
Q ss_pred EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHh
Q psy11278 148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVV 217 (238)
Q Consensus 148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 217 (238)
++..+.+|..+++.+.|++|.+|+.++.+|.++|.-|.... +..|.++|.++.|..|++.|..
T Consensus 26 vt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e-------ePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 26 VTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE-------EPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred cceeeecCcccceeecccCccccchhhhhhcceeccCCCCC-------CCcceeccCchhHHHHhhcCcc
Confidence 55889999999999999999999999999999999997653 4799999999999999999887
No 45
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.39 E-value=0.00034 Score=67.25 Aligned_cols=87 Identities=16% Similarity=0.401 Sum_probs=67.5
Q ss_pred hHHHHHHHHHHHHHhhcc-------ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCe-EEccCCCCCCCCCCc
Q psy11278 124 VERVKEATTKLIEHMCGS-------LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQ-IVFPEANDPIIPVLK 195 (238)
Q Consensus 124 v~~a~~ai~~~~~~~~~~-------~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~-I~~p~~~~~~~~~~~ 195 (238)
...|+++...+++.+.+. +....+....+.||++.++.|||.||.+|++|.++||+. |.+-+
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------- 723 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC----------
Confidence 355556666666655432 222334568899999999999999999999999999999 77654
Q ss_pred ceEEEEEc-CHHHHHHHHHHHHhhcC
Q psy11278 196 KSSVTVSG-NIDSVYLARQMLVVSSV 220 (238)
Q Consensus 196 ~~~v~I~G-~~~~v~~A~~~I~~~l~ 220 (238)
...|.|.| ..+.+++|+.+|..+..
T Consensus 724 dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 724 DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 25788888 59999999999998873
No 46
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.38 E-value=0.00014 Score=69.88 Aligned_cols=60 Identities=32% Similarity=0.494 Sum_probs=53.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCE-EEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCH-VHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP 70 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~-I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~ 70 (238)
.+.||.+.++.|||.||.+|+.|.++||+. |++.+ +..|.|.+ +.+.++.|+++|..+..
T Consensus 688 ~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 688 IMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred EEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 578999999999999999999999999999 99865 36888888 78999999999988754
No 47
>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=97.22 E-value=0.0004 Score=44.86 Aligned_cols=33 Identities=18% Similarity=0.334 Sum_probs=30.7
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEe
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHF 34 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i 34 (238)
.+.||.+..|..|||+|.||+.+++.++-+|++
T Consensus 28 ~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 28 RVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred EEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999988876
No 48
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.20 E-value=0.0081 Score=48.66 Aligned_cols=105 Identities=12% Similarity=0.152 Sum_probs=79.8
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCceEE--EeecCc
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLIFC--FEYPLM 80 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~--~~~p~~ 80 (238)
+.++......+...+|..++.|....|++|.+.. ..+.+.|+|+...++.+...|.+++....+ ++++..
T Consensus 30 v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--------~~~~i~I~g~k~~~~~i~~~i~~~l~~i~~~~i~l~~~ 101 (210)
T PF14611_consen 30 VWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--------SENRIRITGTKSTAEYIEASINEILSNIRTEEIDLSPI 101 (210)
T ss_pred EEecchheeeeecCCchHHHHHHHhcCceEEEec--------CCcEEEEEccHHHHHHHHHHHHHHHhhcEEEEEecchh
Confidence 4567778889999999999999889999999977 346999999999999999999999876644 444432
Q ss_pred CC------CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEc
Q psy11278 81 GS------TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKG 119 (238)
Q Consensus 81 ~~------~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G 119 (238)
.. ........++.+++.+++.+...+. ...+.|.+
T Consensus 102 ~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----~~~~~i~~ 142 (210)
T PF14611_consen 102 ISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----GNKLKISW 142 (210)
T ss_pred hhhhcccccccccHHHHHHHHHHHcEEEEECCC----CCeEEEEE
Confidence 21 0112467789999999999887653 23455554
No 49
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.20 E-value=0.0023 Score=48.46 Aligned_cols=34 Identities=18% Similarity=0.283 Sum_probs=30.7
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~ 183 (238)
..+.+++...+..|||+|++++.++.-+|-++.+
T Consensus 101 ~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 101 AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 6778899999999999999999999999988755
No 50
>KOG2814|consensus
Probab=97.20 E-value=0.00033 Score=59.26 Aligned_cols=75 Identities=13% Similarity=0.130 Sum_probs=60.6
Q ss_pred EEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhcCC---CCc
Q psy11278 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSSVR---PRR 224 (238)
Q Consensus 149 ~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~---~~p 224 (238)
...+.+++.+.++|+|++|.+-++|+++|++.|.+|.+.+. ...++|+| +.++|.+|..+|..++.. ..|
T Consensus 58 ~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n------~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p 131 (345)
T KOG2814|consen 58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN------KEEIKIIGISRNCVIQALERIAKLIDSDRKSFP 131 (345)
T ss_pred hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC------cceEEEeehhHHHHHHHHHHHHHHHHhhhhcCc
Confidence 35678899999999999999999999999999999998854 24555555 799999999999998843 345
Q ss_pred eEEEE
Q psy11278 225 RLLLI 229 (238)
Q Consensus 225 ~~~~~ 229 (238)
+.+..
T Consensus 132 ~thfl 136 (345)
T KOG2814|consen 132 ITHFL 136 (345)
T ss_pred hhhhh
Confidence 44443
No 51
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.19 E-value=0.00052 Score=63.52 Aligned_cols=61 Identities=31% Similarity=0.467 Sum_probs=54.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeC-HHHHHHHHHHHHhhCCc
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELTPL 71 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~~~~ 71 (238)
++.|+.+.++-+||++|++|++|.++||++|++.+ +..|.|.+. .+.+.+|+..|..+..+
T Consensus 555 t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 555 TIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred EEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 57789999999999999999999999999999973 368999885 58999999999998754
No 52
>KOG0336|consensus
Probab=97.17 E-value=0.00033 Score=61.28 Aligned_cols=58 Identities=21% Similarity=0.352 Sum_probs=48.3
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHH
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVR 66 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 66 (238)
+.|-++.+|.+||++|++|+.||..|+++|++.+-+ .+..|+|.|...--.+|+..|.
T Consensus 51 f~iks~mvg~vigrggskik~iq~~tnt~iqii~~~------~e~kv~ifg~~~m~~kaka~id 108 (629)
T KOG0336|consen 51 FSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD------LEVKVTIFGINHMRKKAKASID 108 (629)
T ss_pred hhhhhhhhheeeccCcchhhhhhcccceeEEEeccC------ceeEEEEechHHHHHHHHhhHh
Confidence 456778899999999999999999999999998743 3568999998776667777663
No 53
>KOG0336|consensus
Probab=97.12 E-value=0.00037 Score=60.99 Aligned_cols=63 Identities=16% Similarity=0.134 Sum_probs=55.5
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
..+.|.+.++|.+||++|++|++|+..|+++|++.+-.. +..|+|-|..+--.+|+..|....
T Consensus 49 lcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~-------e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 49 LCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDL-------EVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred hhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCc-------eeEEEEechHHHHHHHHhhHhhhh
Confidence 678888899999999999999999999999999876442 578999999998888888887766
No 54
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.06 E-value=0.0011 Score=54.82 Aligned_cols=62 Identities=21% Similarity=0.333 Sum_probs=53.9
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCCce
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTPLI 72 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~~ 72 (238)
.+.||.+.++.+||++|.+|+.|.++|++.|.+-. ...|.|.| +.+++..|...|+.+..+.
T Consensus 148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 47899999999999999999999999999999954 36899998 5679999999998775543
No 55
>PRK00106 hypothetical protein; Provisional
Probab=97.04 E-value=0.0014 Score=60.15 Aligned_cols=60 Identities=27% Similarity=0.390 Sum_probs=51.6
Q ss_pred EEEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278 2 KLDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT 69 (238)
Q Consensus 2 ~i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~ 69 (238)
.|.+|++.+ |.||||.|.||+.++.-|||-+-|.+ ....|+++| +|-.-+-|+..|..+.
T Consensus 228 ~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--------tp~~v~lS~fdpvRReiAr~~le~Li 289 (535)
T PRK00106 228 TVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--------TPEVVVLSGFDPIRREIARMTLESLI 289 (535)
T ss_pred eEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--------CCCeEEEeCCChHHHHHHHHHHHHHH
Confidence 367899766 99999999999999999999999977 346899999 8888888888886654
No 56
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.03 E-value=0.0014 Score=60.18 Aligned_cols=60 Identities=25% Similarity=0.393 Sum_probs=51.1
Q ss_pred EEEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278 2 KLDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT 69 (238)
Q Consensus 2 ~i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~ 69 (238)
.|.+|++.+ |.||||.|-||+.++.-|||-|=|.+ ....|+|+| +|-.-+-|+..|..+.
T Consensus 207 ~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~fdp~rreia~~~l~~li 268 (514)
T TIGR03319 207 VVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPVRREIARMALEKLI 268 (514)
T ss_pred eEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--------CCCeEEecCCchHHHHHHHHHHHHHH
Confidence 367899766 99999999999999999999999977 346899999 8888888888776654
No 57
>PRK00106 hypothetical protein; Provisional
Probab=96.96 E-value=0.0046 Score=56.76 Aligned_cols=73 Identities=16% Similarity=0.282 Sum_probs=57.8
Q ss_pred HhhccccccceEEEEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHH
Q psy11278 137 HMCGSLANQTSVIMMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQM 214 (238)
Q Consensus 137 ~~~~~~~~~~~~~~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~ 214 (238)
+...+..+..++ ..|.+|++ +-|.|||+.|.+|+-+..-||+.+.+.+.. ..|+|+| .|---+.|+..
T Consensus 215 r~a~~~~~e~tv-s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp---------~~v~lS~fdpvRReiAr~~ 284 (535)
T PRK00106 215 RLAGEYVTEQTI-TTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTP---------EVVVLSGFDPIRREIARMT 284 (535)
T ss_pred Hhcchhhhhhee-eeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCC---------CeEEEeCCChHHHHHHHHH
Confidence 333333333343 67889985 889999999999999999999999997643 5788999 58888889999
Q ss_pred HHhhc
Q psy11278 215 LVVSS 219 (238)
Q Consensus 215 I~~~l 219 (238)
|+.++
T Consensus 285 le~Li 289 (535)
T PRK00106 285 LESLI 289 (535)
T ss_pred HHHHH
Confidence 98888
No 58
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.95 E-value=0.0032 Score=58.44 Aligned_cols=96 Identities=21% Similarity=0.335 Sum_probs=72.0
Q ss_pred EEEEEccccch-----HHHHHHHHHHHHHhhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeE
Q psy11278 114 LVMVKGCEKDV-----ERVKEATTKLIEHMCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181 (238)
Q Consensus 114 ~v~I~G~~~~v-----~~a~~ai~~~~~~~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I 181 (238)
.+.|.|-...+ ..|+.+...+++.+.+.. ....+...++.|++...+-+||++|.+|++|.++|||.|
T Consensus 506 DiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~I 585 (692)
T COG1185 506 DIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKI 585 (692)
T ss_pred eeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEE
Confidence 45666766432 455666666666554322 112233478899999999999999999999999999999
Q ss_pred EccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHhhc
Q psy11278 182 VFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVVSS 219 (238)
Q Consensus 182 ~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l 219 (238)
.+.+ ...|.|.++ .+.+++|+..|..+.
T Consensus 586 died----------dGtv~i~~s~~~~~~~ak~~I~~i~ 614 (692)
T COG1185 586 DIED----------DGTVKIAASDGESAKKAKERIEAIT 614 (692)
T ss_pred EecC----------CCcEEEEecchHHHHHHHHHHHHHH
Confidence 9973 257899997 588899999999987
No 59
>PRK12704 phosphodiesterase; Provisional
Probab=96.93 E-value=0.0022 Score=58.92 Aligned_cols=60 Identities=25% Similarity=0.403 Sum_probs=50.2
Q ss_pred EEEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278 2 KLDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT 69 (238)
Q Consensus 2 ~i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~ 69 (238)
.|.+|++.+ |.||||.|-||+.++.-|||-|-|.+ ....|.++| +|..-+.|+..|..+.
T Consensus 213 ~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--------tp~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 213 VVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--------TPEAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred eeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--------CCCeEEEecCChhhHHHHHHHHHHHH
Confidence 367899766 99999999999999999999999977 346899999 7777777777776653
No 60
>PRK12704 phosphodiesterase; Provisional
Probab=96.93 E-value=0.0044 Score=57.00 Aligned_cols=61 Identities=16% Similarity=0.245 Sum_probs=50.9
Q ss_pred EEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhc
Q psy11278 150 MMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSS 219 (238)
Q Consensus 150 ~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l 219 (238)
..|.+|++ +-|.|||+.|-+|+-+..-||+.|.+.+.. ..|.|+| .|---+.|+..|+.++
T Consensus 212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp---------~~v~ls~~~~~rre~a~~~l~~l~ 274 (520)
T PRK12704 212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---------EAVILSGFDPIRREIARLALEKLV 274 (520)
T ss_pred eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCC---------CeEEEecCChhhHHHHHHHHHHHH
Confidence 67889885 789999999999999999999999997642 6788999 4666567888777776
No 61
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.92 E-value=0.0043 Score=56.97 Aligned_cols=61 Identities=16% Similarity=0.249 Sum_probs=52.8
Q ss_pred EEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEc-CHHHHHHHHHHHHhhc
Q psy11278 150 MMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG-NIDSVYLARQMLVVSS 219 (238)
Q Consensus 150 ~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~l 219 (238)
..|.+|++ +-|.|||+.|-+|+-+..-||+.|.+.+.. ..|+|+| .|---+.|+.-|+.++
T Consensus 206 ~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp---------~~v~ls~fdp~rreia~~~l~~li 268 (514)
T TIGR03319 206 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTP---------EAVILSGFDPVRREIARMALEKLI 268 (514)
T ss_pred eeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCC---------CeEEecCCchHHHHHHHHHHHHHH
Confidence 67899985 789999999999999999999999997643 5788999 5777788999998888
No 62
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.90 E-value=0.00079 Score=64.00 Aligned_cols=60 Identities=30% Similarity=0.487 Sum_probs=52.5
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP 70 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~ 70 (238)
.+.||.+.++.+||.||.+|++|.++||++|++.+ +..|.|.+ +.+.+++|+..|..+..
T Consensus 557 ~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---------~G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 557 TIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---------DGTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred eecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence 46688899999999999999999999999998854 46888888 68999999999988764
No 63
>KOG0119|consensus
Probab=96.73 E-value=0.0058 Score=54.47 Aligned_cols=66 Identities=18% Similarity=0.175 Sum_probs=48.9
Q ss_pred CCeeeEEecCCCchHHHHHHHhCCeEEccCCC---------C-CC-CC-CCcceEEEEEc-CHHHHHHHHHHHHhhcCC
Q psy11278 156 PQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN---------D-PI-IP-VLKKSSVTVSG-NIDSVYLARQMLVVSSVR 221 (238)
Q Consensus 156 ~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~---------~-~~-~~-~~~~~~v~I~G-~~~~v~~A~~~I~~~l~~ 221 (238)
-+|+|+|||..|.+.|+|+++|||+|.|=... + .+ .. +.+.=-+.|++ +.|.|++|...|+.+|+.
T Consensus 152 ~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 152 INFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQS 230 (554)
T ss_pred cceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHh
Confidence 45889999999999999999999999774311 0 00 00 11223577777 599999999999999943
No 64
>KOG1588|consensus
Probab=96.68 E-value=0.002 Score=53.05 Aligned_cols=38 Identities=29% Similarity=0.473 Sum_probs=32.5
Q ss_pred EEEecCC------ccceeeccCCccHHHHHHHcCCEEEecCCCC
Q psy11278 2 KLDVSYT------DHSHIIGRGGLTIKKVMEETGCHVHFPDSNR 39 (238)
Q Consensus 2 ~i~ip~~------~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~ 39 (238)
+|.||-+ ++|.|+|.+|.++|+|+++|||+|.|-...+
T Consensus 95 Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgS 138 (259)
T KOG1588|consen 95 KVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGS 138 (259)
T ss_pred EEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCc
Confidence 4566654 7899999999999999999999999987654
No 65
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.65 E-value=0.004 Score=59.32 Aligned_cols=87 Identities=18% Similarity=0.320 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHhhccc-------cccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcce
Q psy11278 125 ERVKEATTKLIEHMCGSL-------ANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKS 197 (238)
Q Consensus 125 ~~a~~ai~~~~~~~~~~~-------~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~ 197 (238)
+.|+++...+++.+...+ ....+....+.||+...+.+||.||.+|++|.++||+.|.+-+ ..
T Consensus 524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d----------~G 593 (693)
T PRK11824 524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----------DG 593 (693)
T ss_pred HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC----------Cc
Confidence 455556666666554332 1122334677889999999999999999999999999877632 35
Q ss_pred EEEEEc-CHHHHHHHHHHHHhhcCC
Q psy11278 198 SVTVSG-NIDSVYLARQMLVVSSVR 221 (238)
Q Consensus 198 ~v~I~G-~~~~v~~A~~~I~~~l~~ 221 (238)
.|.|.+ ..+.+++|+++|..+...
T Consensus 594 ~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 594 TVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred eEEEEcccHHHHHHHHHHHHHhccc
Confidence 788888 589999999999998843
No 66
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.64 E-value=0.004 Score=40.14 Aligned_cols=34 Identities=12% Similarity=0.147 Sum_probs=31.5
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~ 183 (238)
..+.+++...+..||++|.+|+.+++.+|-+|.+
T Consensus 27 ~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 27 ARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred EEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 7889999999999999999999999999987764
No 67
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.41 E-value=0.0062 Score=50.33 Aligned_cols=62 Identities=16% Similarity=0.284 Sum_probs=53.6
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHHHHHHHHHhhcCC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVYLARQMLVVSSVR 221 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~~A~~~I~~~l~~ 221 (238)
..+.||..+++.+||++|..|+.|.+.+++.|.+-. ...|.|.|+ .+++.+|..+|+.+-..
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~----------NG~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ----------NGRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC----------CcEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 568889999999999999999999999999999854 257999996 66899999999887643
No 68
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=96.16 E-value=0.12 Score=41.88 Aligned_cols=113 Identities=12% Similarity=0.150 Sum_probs=79.8
Q ss_pred CCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEEeCCCeeeEEe-c
Q psy11278 86 ANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIME-G 164 (238)
Q Consensus 86 ~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~i~~~~~~~iI-G 164 (238)
.++..++.+...+|++|.+... ...+.|+|++..++.+...+..++.. . .+..|.++.-...+-- +
T Consensus 43 ~~~~~L~~l~~~~~~~I~~~~~----~~~i~I~g~k~~~~~i~~~i~~~l~~----i-----~~~~i~l~~~~~~~~~~~ 109 (210)
T PF14611_consen 43 GNGRILENLAARNGAKIEVSRS----ENRIRITGTKSTAEYIEASINEILSN----I-----RTEEIDLSPIISKHSEKK 109 (210)
T ss_pred CCchHHHHHHHhcCceEEEecC----CcEEEEEccHHHHHHHHHHHHHHHhh----c-----EEEEEecchhhhhhcccc
Confidence 4678889997788999998763 36899999988887777666666652 2 2245555533211111 1
Q ss_pred ---CCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEE-----cCHHHHHHHHHHHHhhcC
Q psy11278 165 ---PNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVS-----GNIDSVYLARQMLVVSSV 220 (238)
Q Consensus 165 ---~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~-----G~~~~v~~A~~~I~~~l~ 220 (238)
.....++.|++.|++.|....+. ..+.|. -.+.....|+++|...+.
T Consensus 110 ~~~~~~~~l~~i~~~t~~~ie~~~~~---------~~~~i~~~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 110 NSQFTPDLLEEIQKLTNVYIEKNPDG---------NKLKISWLASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred cccccHHHHHHHHHHHcEEEEECCCC---------CeEEEEEEeeccccchHHHHHHHHHHhcc
Confidence 13677899999999999987654 234444 468899999999999994
No 69
>PRK12705 hypothetical protein; Provisional
Probab=96.12 E-value=0.0051 Score=56.13 Aligned_cols=59 Identities=25% Similarity=0.359 Sum_probs=46.4
Q ss_pred EEecCCcc-ceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhC
Q psy11278 3 LDVSYTDH-SHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELT 69 (238)
Q Consensus 3 i~ip~~~~-g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~ 69 (238)
+.+|++.+ |.||||.|.||+.++..||+.+-|.+. ...|++++ +|..-+.|+..++.++
T Consensus 202 v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--------p~~V~ls~fdp~rreia~~~l~~Li 262 (508)
T PRK12705 202 VPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT--------PEAVVISSFNPIRREIARLTLEKLL 262 (508)
T ss_pred eecCChHhhccccCccchhHHHHHHhhCCceEecCC--------ccchhhcccCccchHHHHHHHHHHH
Confidence 67888766 999999999999999999999999773 34666776 5666666666665553
No 70
>KOG1067|consensus
Probab=96.11 E-value=0.018 Score=52.45 Aligned_cols=95 Identities=16% Similarity=0.251 Sum_probs=71.4
Q ss_pred hHHHHHHHHHHHHHhhcccc-------ccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcc
Q psy11278 124 VERVKEATTKLIEHMCGSLA-------NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKK 196 (238)
Q Consensus 124 v~~a~~ai~~~~~~~~~~~~-------~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~ 196 (238)
..+|+.+..++++.+..+.. .+.++...+.++++....+||.+|.+.|+|..+||+.-.+. +
T Consensus 566 l~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-----------e 634 (760)
T KOG1067|consen 566 LQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-----------E 634 (760)
T ss_pred HHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec-----------C
Confidence 45566677778887765432 12345688899999999999999999999999999654442 3
Q ss_pred eEEEEEcC-HHHHHHHHHHHHhhcCCCCceEEEE
Q psy11278 197 SSVTVSGN-IDSVYLARQMLVVSSVRPRRRLLLI 229 (238)
Q Consensus 197 ~~v~I~G~-~~~v~~A~~~I~~~l~~~~p~~~~~ 229 (238)
..++|.-+ +++.++|+..|.+++..+.-..|.|
T Consensus 635 ~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~ 668 (760)
T KOG1067|consen 635 GTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEF 668 (760)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHhcCccccceEe
Confidence 56888775 8888999999999997654444444
No 71
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=95.97 E-value=0.025 Score=50.90 Aligned_cols=113 Identities=14% Similarity=0.127 Sum_probs=74.8
Q ss_pred eeeccCCccHHHHHHHcCCE--EEecCCCCCCCCCCCCeEE-EEeCHHHHHHHHHHHHhhCCceEEEeecCcCC--CCCC
Q psy11278 12 HIIGRGGLTIKKVMEETGCH--VHFPDSNRSVNAEKSNQVS-IAGSLLGLERARYRVRELTPLIFCFEYPLMGS--TPNA 86 (238)
Q Consensus 12 ~IIGk~G~~I~~I~~~t~~~--I~i~~~~~~~~~~~~~~v~-I~G~~~~v~~A~~~I~~~~~~~~~~~~p~~~~--~~~~ 86 (238)
++=||+.-++.+||+...|. +.+.++++ +.+.+ +.|..-+..++.+.+..-.|+..+|-+|..++ .+|.
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~g------s~~~~~~~g~~~~F~k~~~~~~~EFpae~~f~i~e~~h~~IIgt 466 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSSTG------SIVETNGIGEKMSFSKKLSIPPTEFPAEIAFIIMESGHEMIIGT 466 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecCC------cEEEEeccCcchhhHHHhcCCcccCchheEEEeecccceeeecc
Confidence 66788877799999999888 45555432 23222 34666666666666655555556777776654 6788
Q ss_pred CChHHHHHHHHhCceEEeeCC---CCCC-CcEEEEEccccchHHHHHH
Q psy11278 87 NSPFVQIIQEAYNVQVMFRNR---PKLQ-PTLVMVKGCEKDVERVKEA 130 (238)
Q Consensus 87 ~g~~i~~i~~~~gv~I~~~~~---~~~~-~~~v~I~G~~~~v~~a~~a 130 (238)
+|..|++.+.+++|.|.|... +.+. .+.|.|+-+.+|.+....+
T Consensus 467 gG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~ 514 (657)
T COG5166 467 GGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGK 514 (657)
T ss_pred CchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcc
Confidence 999999999999999988652 2221 2346666666655444433
No 72
>KOG1588|consensus
Probab=95.94 E-value=0.012 Score=48.59 Aligned_cols=72 Identities=17% Similarity=0.192 Sum_probs=48.8
Q ss_pred EEEEEEeCC------CeeeEEecCCCchHHHHHHHhCCeEEccCCC-------------CCCCCCCc---ceEEEEEcCH
Q psy11278 148 VIMMMEISP------QHHPIMEGPNAINLKTIMAQTGAQIVFPEAN-------------DPIIPVLK---KSSVTVSGNI 205 (238)
Q Consensus 148 ~~~~v~i~~------~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~-------------~~~~~~~~---~~~v~I~G~~ 205 (238)
++..|.||- +|+|.|+|..|.++++++++|||+|.+=... ++++.... .-.|...+++
T Consensus 92 ~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~p~ 171 (259)
T KOG1588|consen 92 LTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEAPP 171 (259)
T ss_pred EEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeCCH
Confidence 445555554 4899999999999999999999999774322 11111111 2367777776
Q ss_pred HHHH----HHHHHHHhhc
Q psy11278 206 DSVY----LARQMLVVSS 219 (238)
Q Consensus 206 ~~v~----~A~~~I~~~l 219 (238)
+-+. .|...|+.+|
T Consensus 172 ~ea~~rl~~AleeI~klL 189 (259)
T KOG1588|consen 172 AEAYARLAYALEEIKKLL 189 (259)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 6555 4777788777
No 73
>PRK12705 hypothetical protein; Provisional
Probab=95.92 E-value=0.02 Score=52.40 Aligned_cols=79 Identities=16% Similarity=0.212 Sum_probs=56.6
Q ss_pred HHHHHHhhccccccceEEEEEEeCCC-eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcC-HHHHH
Q psy11278 132 TKLIEHMCGSLANQTSVIMMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN-IDSVY 209 (238)
Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~-~~~v~ 209 (238)
...+++...+..+..++ ..|.+|++ +-|.|||+.|.+|+-+...||+.+.+.+.. ..|+|.+. |.--+
T Consensus 183 ~~aiqr~a~~~~~e~tv-s~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp---------~~V~ls~fdp~rre 252 (508)
T PRK12705 183 AQAMQRIASETASDLSV-SVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTP---------EAVVISSFNPIRRE 252 (508)
T ss_pred HHHHHHhccchhhhhee-eeeecCChHhhccccCccchhHHHHHHhhCCceEecCCc---------cchhhcccCccchH
Confidence 33344444444333343 57788875 779999999999999999999999997643 45777774 66666
Q ss_pred HHHHHHHhhcC
Q psy11278 210 LARQMLVVSSV 220 (238)
Q Consensus 210 ~A~~~I~~~l~ 220 (238)
.|+..+..++.
T Consensus 253 ia~~~l~~Li~ 263 (508)
T PRK12705 253 IARLTLEKLLA 263 (508)
T ss_pred HHHHHHHHHHh
Confidence 77877777773
No 74
>PRK00468 hypothetical protein; Provisional
Probab=95.24 E-value=0.014 Score=39.28 Aligned_cols=26 Identities=27% Similarity=0.411 Sum_probs=23.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHH
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEE 27 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~ 27 (238)
++.+..+..|.+|||+|.+++.|+.-
T Consensus 33 ~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 33 ELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred EEEEChhhCcceecCCChhHHHHHHH
Confidence 57788999999999999999999853
No 75
>PRK02821 hypothetical protein; Provisional
Probab=95.07 E-value=0.015 Score=39.19 Aligned_cols=28 Identities=29% Similarity=0.430 Sum_probs=24.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETG 29 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~ 29 (238)
.+.+.++..|.+|||+|.+++.|+.--.
T Consensus 34 ~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 34 EVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred EEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 5778899999999999999999986543
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.04 E-value=0.03 Score=44.59 Aligned_cols=32 Identities=19% Similarity=0.219 Sum_probs=28.8
Q ss_pred CCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278 7 YTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN 38 (238)
Q Consensus 7 ~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~ 38 (238)
.+++|.|||..|+|+++|+..|+|+|.|-...
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 35789999999999999999999999997754
No 77
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.02 E-value=0.018 Score=38.60 Aligned_cols=25 Identities=32% Similarity=0.525 Sum_probs=22.5
Q ss_pred EEEecCCccceeeccCCccHHHHHH
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVME 26 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~ 26 (238)
++.+.++..|.+|||+|.+++.|+-
T Consensus 33 ~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 33 ELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred EEEECcccccceecCCChhHHHHHH
Confidence 5678889999999999999999985
No 78
>PRK01064 hypothetical protein; Provisional
Probab=94.67 E-value=0.029 Score=38.00 Aligned_cols=26 Identities=38% Similarity=0.512 Sum_probs=23.3
Q ss_pred EEEecCCccceeeccCCccHHHHHHH
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEE 27 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~ 27 (238)
++.+.++..|.+|||+|.+|+.|+.-
T Consensus 33 ~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 33 ELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred EEEECcccceEEECCCCccHHHHHHH
Confidence 57788999999999999999999874
No 79
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.05 E-value=0.094 Score=41.83 Aligned_cols=32 Identities=19% Similarity=0.302 Sum_probs=28.3
Q ss_pred CCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278 156 PQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN 187 (238)
Q Consensus 156 ~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~ 187 (238)
.+|+|+|||..|.+.++++..|+|+|.+-...
T Consensus 162 ~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 162 SNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred cceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 46999999999999999999999999875443
No 80
>KOG4369|consensus
Probab=93.97 E-value=0.022 Score=55.89 Aligned_cols=64 Identities=17% Similarity=0.170 Sum_probs=54.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHh
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRE 67 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~ 67 (238)
++.+|....+.+||++|+||..++.-||+.|++.+.... +..+|.+.+.|.++.+..|...|.-
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~--Nqaers~~~kg~p~~~r~a~~~I~~ 1406 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPD--NQAERSKAPKGRPPSQRVATSPIGL 1406 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCc--cchhhhcccCCCChhhhhhhccccc
Confidence 467888889999999999999999999999999874431 2357899999999999999988843
No 81
>KOG2874|consensus
Probab=93.44 E-value=0.13 Score=42.87 Aligned_cols=52 Identities=29% Similarity=0.402 Sum_probs=46.6
Q ss_pred cceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL 71 (238)
Q Consensus 10 ~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~ 71 (238)
+..+||.+|+|++.|+--|+|.|-+.. ..|.+.|...++..++..+.+++..
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVqG----------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQG----------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEeeC----------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 457899999999999999999999965 6899999999999999999887653
No 82
>PRK00468 hypothetical protein; Provisional
Probab=93.34 E-value=0.11 Score=34.90 Aligned_cols=32 Identities=22% Similarity=0.286 Sum_probs=27.5
Q ss_pred EEEEEEeCCCeeeEEecCCCchHHHHHHHhCC
Q psy11278 148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGA 179 (238)
Q Consensus 148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga 179 (238)
...++.+.+.-.|.+|||+|.+|+.|+.--.+
T Consensus 30 ~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~a 61 (75)
T PRK00468 30 VILELKVAPEDMGKVIGKQGRIAKAIRTVVKA 61 (75)
T ss_pred EEEEEEEChhhCcceecCCChhHHHHHHHHHH
Confidence 45788999999999999999999999986443
No 83
>KOG1067|consensus
Probab=93.32 E-value=0.087 Score=48.13 Aligned_cols=59 Identities=27% Similarity=0.374 Sum_probs=50.0
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEe-CHHHHHHHHHHHHhhCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAG-SLLGLERARYRVRELTP 70 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~ 70 (238)
.+.++.+.+..+||.+|.+.|+|+.|||+.-.+ ++..++|.. ++...+.|++.|..+..
T Consensus 600 tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v----------De~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 600 TLKVSPSKRATLIGPGGVLKKKIEVETGAISQV----------DEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred EEeecchhhheeecCccceeeeEeeeccceeee----------cCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 477999999999999999999999999955555 346888887 68899999999987754
No 84
>KOG2874|consensus
Probab=93.31 E-value=0.13 Score=42.91 Aligned_cols=55 Identities=18% Similarity=0.214 Sum_probs=48.7
Q ss_pred eEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCce
Q psy11278 160 PIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRR 225 (238)
Q Consensus 160 ~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p~ 225 (238)
..+||.+|++++.|+--|.|.|-+.. ..|.+.|+..++..+++.+.+.|.--+|+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-----------~TVsaiGpfkGlkevr~IV~DcM~NiHPi 215 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-----------NTVSAIGPFKGLKEVRKIVEDCMKNIHPI 215 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-----------cEEEeecCcchHHHHHHHHHHHHhccchH
Confidence 46899999999999999999999863 67999999999999999999998665554
No 85
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=93.00 E-value=0.13 Score=33.13 Aligned_cols=28 Identities=18% Similarity=0.252 Sum_probs=23.0
Q ss_pred ecCCccceeeccCCccHHHHHHHcCCEE
Q psy11278 5 VSYTDHSHIIGRGGLTIKKVMEETGCHV 32 (238)
Q Consensus 5 ip~~~~g~IIGk~G~~I~~I~~~t~~~I 32 (238)
+.....|.+||++|.+++.++..++-.+
T Consensus 31 ~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 31 VARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred ECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 3444579999999999999999998554
No 86
>PRK02821 hypothetical protein; Provisional
Probab=92.82 E-value=0.13 Score=34.65 Aligned_cols=33 Identities=9% Similarity=0.110 Sum_probs=28.5
Q ss_pred EEEEEEeCCCeeeEEecCCCchHHHHHHHhCCe
Q psy11278 148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQ 180 (238)
Q Consensus 148 ~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~ 180 (238)
....+.+.+.-.|.+|||+|..|+.|+.--.+.
T Consensus 31 ~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~ 63 (77)
T PRK02821 31 RTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI 63 (77)
T ss_pred EEEEEEEChhhCcceeCCCCchHHHHHHHHHHh
Confidence 347888899999999999999999999885553
No 87
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=92.79 E-value=0.19 Score=33.76 Aligned_cols=31 Identities=13% Similarity=0.281 Sum_probs=27.4
Q ss_pred eEEEEEEeCCCeeeEEecCCCchHHHHHHHh
Q psy11278 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQT 177 (238)
Q Consensus 147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~t 177 (238)
.+..++.+.+.-.|.+|||+|.+|+-|+.--
T Consensus 29 ~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 29 TVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred eEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 4568889999999999999999999999863
No 88
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=92.72 E-value=0.094 Score=34.62 Aligned_cols=28 Identities=29% Similarity=0.408 Sum_probs=23.0
Q ss_pred cceeeccCCccHHHHHHHc-CCEEEecCC
Q psy11278 10 HSHIIGRGGLTIKKVMEET-GCHVHFPDS 37 (238)
Q Consensus 10 ~g~IIGk~G~~I~~I~~~t-~~~I~i~~~ 37 (238)
+|..||++|++|+.|+++. |-+|++-.-
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred ceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 7999999999999999999 999988553
No 89
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=92.51 E-value=0.31 Score=39.95 Aligned_cols=59 Identities=19% Similarity=0.339 Sum_probs=49.1
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHH-HHHHHHHHHHhhCC
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLL-GLERARYRVRELTP 70 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~-~v~~A~~~I~~~~~ 70 (238)
+.||+..+..+||++|+.++.|.++|+|.|-+-. ...|-|.|..+ ....|...|+.+..
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---------NG~IWV~~~~~~~e~~~~~aI~~ie~ 209 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---------NGRIWVDGENESLEELAIEAIRKIER 209 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---------CCEEEecCCCcchHHHHHHHHHHHhh
Confidence 6799999999999999999999999999999965 25888888776 46667777776644
No 90
>PRK01064 hypothetical protein; Provisional
Probab=92.48 E-value=0.26 Score=33.35 Aligned_cols=33 Identities=12% Similarity=0.171 Sum_probs=27.9
Q ss_pred eEEEEEEeCCCeeeEEecCCCchHHHHHHHhCC
Q psy11278 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGA 179 (238)
Q Consensus 147 ~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga 179 (238)
.+..++.+.+.-.|.+|||+|.+|+.|+.-.++
T Consensus 29 ~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~ 61 (78)
T PRK01064 29 TIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVS 61 (78)
T ss_pred EEEEEEEECcccceEEECCCCccHHHHHHHHHH
Confidence 345788899999999999999999999986443
No 91
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.43 E-value=0.035 Score=36.95 Aligned_cols=28 Identities=18% Similarity=0.326 Sum_probs=24.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETG 29 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~ 29 (238)
.+.+..+..|.+|||+|.+++.||--.+
T Consensus 32 ~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 32 VVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp EEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred EEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4678888999999999999999997554
No 92
>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=91.78 E-value=0.2 Score=38.00 Aligned_cols=34 Identities=15% Similarity=0.207 Sum_probs=30.2
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~ 183 (238)
..+.+|++..+..||++|++++..++-+|-++.+
T Consensus 102 a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 102 AYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred EEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 6788888999999999999999999999888754
No 93
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=91.33 E-value=0.11 Score=46.66 Aligned_cols=37 Identities=22% Similarity=0.388 Sum_probs=33.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN 38 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~ 38 (238)
-+.+|.+.++.+|||+|.+|++|++..|.+|.+....
T Consensus 489 vv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 489 VVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred EEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 3678999999999999999999999999999996644
No 94
>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=91.30 E-value=0.19 Score=33.78 Aligned_cols=33 Identities=18% Similarity=0.255 Sum_probs=26.9
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEe
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHF 34 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i 34 (238)
.+.+..+..|.+|||+|.++..||--++.-++-
T Consensus 27 ~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 27 EVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 466778889999999999999999877655443
No 95
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.92 E-value=1.2 Score=40.55 Aligned_cols=36 Identities=19% Similarity=0.388 Sum_probs=33.0
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
..+.||...|..|||.||..|++++.+.++.|.|..
T Consensus 451 ~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n 486 (657)
T COG5166 451 IAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKN 486 (657)
T ss_pred eEEEeecccceeeeccCchhhHHhhhhhhhhhhhhh
Confidence 678999999999999999999999999999987643
No 96
>PRK13764 ATPase; Provisional
Probab=90.81 E-value=0.14 Score=47.92 Aligned_cols=37 Identities=27% Similarity=0.451 Sum_probs=33.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN 38 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~ 38 (238)
.+.||.+.++.+|||+|.+|.+|+++.|.+|++....
T Consensus 484 ~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~ 520 (602)
T PRK13764 484 VVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLD 520 (602)
T ss_pred EEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEcc
Confidence 4679999999999999999999999999999996644
No 97
>KOG3273|consensus
Probab=90.62 E-value=0.18 Score=40.09 Aligned_cols=50 Identities=26% Similarity=0.369 Sum_probs=45.4
Q ss_pred ccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278 9 DHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 68 (238)
.+|.|+||+|.+--.|++-|.++|.+.+ ..|-|-|..+++..|+..+..+
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad----------~kIHiLG~~~niriAR~avcsL 228 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD----------SKIHILGAFQNIRIARDAVCSL 228 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC----------ceEEEeecchhhHHHHHhhHhh
Confidence 4689999999999999999999999965 5899999999999999999765
No 98
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=90.40 E-value=0.35 Score=36.64 Aligned_cols=36 Identities=17% Similarity=0.280 Sum_probs=31.2
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
.-+-+++..+|..||++|++|+.|++..|-+|.+-.
T Consensus 34 vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 34 IIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred EEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEE
Confidence 566778889999999999999999999998886544
No 99
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.36 E-value=0.77 Score=37.69 Aligned_cols=47 Identities=21% Similarity=0.420 Sum_probs=39.6
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHH
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~ 206 (238)
.-+.|++..+..+||++|+.++-+.++++|.|.+-.. ..|-+.|..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N----------G~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN----------GRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC----------CEEEecCCCc
Confidence 5688999999999999999999999999999998653 3566666655
No 100
>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=90.08 E-value=0.1 Score=35.12 Aligned_cols=31 Identities=26% Similarity=0.401 Sum_probs=25.4
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEE
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVH 33 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~ 33 (238)
+.+-.++-+.+||++|++|++|.++.+-.+.
T Consensus 29 i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 29 IVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred EEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 5567778899999999999999987765553
No 101
>KOG4369|consensus
Probab=88.70 E-value=0.18 Score=49.91 Aligned_cols=67 Identities=15% Similarity=0.013 Sum_probs=53.6
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSS 219 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l 219 (238)
..+.+|-+...++||++|++|+.++.-|||.|.+.+-...+- .++.+.+.|.++.+..|...|--.+
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nq---aers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQ---AERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccc---hhhhcccCCCChhhhhhhcccccee
Confidence 456777788899999999999999999999999876332221 3789999999999998886665444
No 102
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=88.60 E-value=0.47 Score=36.93 Aligned_cols=34 Identities=26% Similarity=0.317 Sum_probs=29.0
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecCC
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDS 37 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~ 37 (238)
+.|-... |.-|||+|.+++++++..|-+|.+-..
T Consensus 65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 4455666 999999999999999999999988653
No 103
>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=88.59 E-value=0.23 Score=33.91 Aligned_cols=35 Identities=17% Similarity=0.402 Sum_probs=28.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD 36 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~ 36 (238)
++.|-...-|.+||++|++|++|+++..-...++.
T Consensus 33 ~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 33 EIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 46677777899999999999999998876666643
No 104
>KOG3273|consensus
Probab=88.50 E-value=0.28 Score=38.98 Aligned_cols=56 Identities=16% Similarity=0.211 Sum_probs=48.8
Q ss_pred eeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCc
Q psy11278 158 HHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRR 224 (238)
Q Consensus 158 ~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p 224 (238)
.+|.|.|++|.+---|++.|-++|.+.+ ..|.|-|..+++..|+..+..++-+.-|
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad-----------~kIHiLG~~~niriAR~avcsLIlGspp 234 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD-----------SKIHILGAFQNIRIARDAVCSLILGSPP 234 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC-----------ceEEEeecchhhHHHHHhhHhhhccCCc
Confidence 4578999999999999999999999864 5799999999999999999998855443
No 105
>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=88.49 E-value=0.8 Score=34.66 Aligned_cols=87 Identities=13% Similarity=0.174 Sum_probs=53.8
Q ss_pred CCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHHhhcccccc--ceEEEEEEeCCCeeeEEe
Q psy11278 86 ANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQ--TSVIMMMEISPQHHPIME 163 (238)
Q Consensus 86 ~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~--~~~~~~v~i~~~~~~~iI 163 (238)
.++..+++|.++.--+|.+.+.|. +.-+ -+.|.+.|.+++-.-+ ...+- ...+-+|.|-...-|.+|
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~dps-------~l~~---~e~A~~~I~~ivP~ea-~i~di~Fd~~tGEV~IeaeKPG~Vi 91 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRPDPS-------VLKP---PEEAIKIILEIVPEEA-GITDIYFDDDTGEVIIEAEKPGLVI 91 (145)
T ss_pred cccHHHHHHHHHHhceEEEcCChh-------hcCC---HHHHHHHHHHhCCCcc-CceeeEecCCCcEEEEEEcCCeEEE
Confidence 356778888888776777654331 1112 2345545555442111 11110 011256777777889999
Q ss_pred cCCCchHHHHHHHhCCeEEc
Q psy11278 164 GPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 164 G~~G~~I~~I~~~tga~I~~ 183 (238)
|++|..+++|..+||-+-.+
T Consensus 92 Gk~g~~~reI~~~tgW~p~v 111 (145)
T cd02410 92 GKGGSTLREITRETGWAPKV 111 (145)
T ss_pred ecCchhHHHHHHHhCCeeEE
Confidence 99999999999999998655
No 106
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=88.22 E-value=0.27 Score=32.39 Aligned_cols=37 Identities=16% Similarity=0.186 Sum_probs=26.0
Q ss_pred EEEeCCCe-----eeEEecCCCchHHHHHHHh-CCeEEccCCC
Q psy11278 151 MMEISPQH-----HPIMEGPNAINLKTIMAQT-GAQIVFPEAN 187 (238)
Q Consensus 151 ~v~i~~~~-----~~~iIG~~G~~I~~I~~~t-ga~I~~p~~~ 187 (238)
.+.+.+.. +|..||++|.+|+.|+++. |-+|.+-..+
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s 48 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS 48 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence 44444444 7899999999999999999 8888765443
No 107
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=87.92 E-value=0.39 Score=42.22 Aligned_cols=37 Identities=19% Similarity=0.344 Sum_probs=33.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSN 38 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~ 38 (238)
.+.||.++.+..|||+|.|++--.+-||.+|+|..-.
T Consensus 311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 4679999999999999999999999999999996643
No 108
>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=86.81 E-value=1.3 Score=28.20 Aligned_cols=32 Identities=6% Similarity=0.228 Sum_probs=25.6
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeE
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I 181 (238)
..+.+.....+.+||++|.+++.++..++-.+
T Consensus 27 ~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 27 IIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 44455544579999999999999999988765
No 109
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.93 E-value=1.1 Score=30.12 Aligned_cols=34 Identities=12% Similarity=0.111 Sum_probs=28.7
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~ 183 (238)
..+.+.....+.+||++|++++.|+--++..++-
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 5677778888999999999999999888776554
No 110
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=85.68 E-value=0.23 Score=32.98 Aligned_cols=32 Identities=13% Similarity=0.191 Sum_probs=27.9
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeE
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQI 181 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I 181 (238)
..+.+.....|.+|||+|.+++.|+.-.+..+
T Consensus 31 i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 31 IVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp EEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred EEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 67888899999999999999999998776654
No 111
>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=85.68 E-value=0.85 Score=34.55 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=30.9
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
.-+.+.+..+|..||++|++|+.+++..|-+|.+-.
T Consensus 35 iifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 35 VVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred EEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 567788889999999999999999988998876543
No 112
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=85.58 E-value=0.6 Score=42.57 Aligned_cols=36 Identities=19% Similarity=0.278 Sum_probs=33.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDS 37 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~ 37 (238)
.+.||.++.+.-|||+|.|++-..+-||.+|+|-..
T Consensus 305 ~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 305 DVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 477999999999999999999999999999999663
No 113
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.08 E-value=0.52 Score=42.45 Aligned_cols=37 Identities=16% Similarity=0.247 Sum_probs=33.8
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEA 186 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~ 186 (238)
+-+.+|..+.+.+|||+|.+|++|+++.|-.|.+-..
T Consensus 488 avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 488 AVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred EEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 6788999999999999999999999999999988543
No 114
>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=83.93 E-value=0.75 Score=31.32 Aligned_cols=36 Identities=14% Similarity=0.251 Sum_probs=29.7
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
.++.|-...-+.+||++|+.|++|++.-.....+++
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 667777777799999999999999998777766644
No 115
>PRK13764 ATPase; Provisional
Probab=83.51 E-value=0.78 Score=43.12 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=33.5
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
+-+.+|..+.+.+|||+|.+|++|.++.|..|.+-.
T Consensus 483 ~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 483 AVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred EEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 778999999999999999999999999999998743
No 116
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=82.91 E-value=0.31 Score=32.72 Aligned_cols=33 Identities=18% Similarity=0.314 Sum_probs=27.9
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEE
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIV 182 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~ 182 (238)
..+.+...+-+.+||++|++|++|....+-.+.
T Consensus 27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 27 IIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 566777788899999999999999998877664
No 117
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=82.49 E-value=10 Score=34.91 Aligned_cols=115 Identities=17% Similarity=0.250 Sum_probs=65.6
Q ss_pred HHHHHHHHHHhhCCc-e----EEEeecCcCC------CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchH
Q psy11278 57 GLERARYRVRELTPL-I----FCFEYPLMGS------TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVE 125 (238)
Q Consensus 57 ~v~~A~~~I~~~~~~-~----~~~~~p~~~~------~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~ 125 (238)
..+.-++.|.+++|. . ..|+=|.+.. .....|..++++.++.--+|.+.+.|.. .-+ -+
T Consensus 6 ~l~ei~~~i~~~~p~~~~It~vefEGPelvvY~k~P~~~~~~~dlik~lAk~lrKRI~iR~dPsv-------l~~---~e 75 (637)
T COG1782 6 VLEEIRNKINEILPSDVKITDVEFEGPELVVYTKNPELFAKDGDLIKDLAKDLRKRIIIRPDPSV-------LKP---PE 75 (637)
T ss_pred HHHHHHHHHHHhCCCcCceEEEEecCCeEEEEecCHHHhccchhHHHHHHHHHhhceEeccCchh-------cCC---HH
Confidence 344556677777774 2 2222243211 1224678899999888777777654421 111 23
Q ss_pred HHHHHHHHHHHHhhcccccc--ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEE
Q psy11278 126 RVKEATTKLIEHMCGSLANQ--TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIV 182 (238)
Q Consensus 126 ~a~~ai~~~~~~~~~~~~~~--~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~ 182 (238)
.|++-|.+++...++ ..+- ...+-+|.|-++.=|.+||++|++.++|..+||-.-.
T Consensus 76 ~A~~~I~eivP~ea~-i~~i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ 133 (637)
T COG1782 76 EARKIILEIVPEEAG-ITDIYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPK 133 (637)
T ss_pred HHHHHHHHhCccccC-ceeEEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcce
Confidence 344333433321111 1000 0012567777777899999999999999999998643
No 118
>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=82.42 E-value=1.3 Score=38.60 Aligned_cols=36 Identities=14% Similarity=0.135 Sum_probs=33.5
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
+.+.+|....+.-||++|.+++-.++-||.+|.+-.
T Consensus 303 ~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 303 AEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 789999999999999999999999999999998754
No 119
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=81.87 E-value=1.2 Score=35.55 Aligned_cols=88 Identities=13% Similarity=0.144 Sum_probs=55.4
Q ss_pred CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHH--HHHHHhhccccccceEEEEEEeCCCeee
Q psy11278 83 TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATT--KLIEHMCGSLANQTSVIMMMEISPQHHP 160 (238)
Q Consensus 83 ~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~--~~~~~~~~~~~~~~~~~~~v~i~~~~~~ 160 (238)
..|++|.+++.++++.|-+|.+-.- +-++ ..-++.++. .++.-...+. + .. .+.+.+|++..+
T Consensus 90 ~iG~~G~rvk~i~~eLgekIdVVe~----------s~d~--~~fI~nal~Pa~v~~V~~~~~-d-~~-~~~v~V~~~~~~ 154 (190)
T COG0195 90 CIGKRGSRVKAVSEELGEKIDVVEW----------SEDP--AEFIKNALAPAEVLSVNIKED-D-GH-VAIVVVPPDQLS 154 (190)
T ss_pred hccCCChHHHHHHHHhCCceEEEEe----------CCCH--HHHHHHhcCcceEeEEEEEeC-C-Cc-EEEEEECHHHHh
Confidence 5688999999999999865554321 0000 111111111 0000000000 0 11 377889999999
Q ss_pred EEecCCCchHHHHHHHhCCeEEccC
Q psy11278 161 IMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 161 ~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
..||++|.+++-.++-||-++.+-.
T Consensus 155 ~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 155 LAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred hccCcccHHHHHHHHHhCCEEEEEe
Confidence 9999999999999999999998754
No 120
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=81.31 E-value=1.4 Score=38.76 Aligned_cols=38 Identities=21% Similarity=0.307 Sum_probs=34.2
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN 187 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~ 187 (238)
+.+.+|....+.-||++|++++-.++-||.+|.+-.-.
T Consensus 310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 78899999999999999999999999999999875433
No 121
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=80.63 E-value=1.2 Score=39.92 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=32.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD 36 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~ 36 (238)
.+.||.++.+.-|||+|.|++--..-||.+|+|.+
T Consensus 338 ~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 338 HVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 46799999999999999999999999999999965
No 122
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=80.49 E-value=1.5 Score=35.00 Aligned_cols=83 Identities=16% Similarity=0.189 Sum_probs=51.6
Q ss_pred ecCCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc-------------
Q psy11278 5 VSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL------------- 71 (238)
Q Consensus 5 ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~------------- 71 (238)
+-.+.+|..||++|++++.|.++.|=+|++-.-++ ++ .+-.++.+. |.
T Consensus 82 ~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~--------------d~--~~fI~nal~---Pa~v~~V~~~~~d~~ 142 (190)
T COG0195 82 VKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSE--------------DP--AEFIKNALA---PAEVLSVNIKEDDGH 142 (190)
T ss_pred cCcCchhhhccCCChHHHHHHHHhCCceEEEEeCC--------------CH--HHHHHHhcC---cceEeEEEEEeCCCc
Confidence 33456799999999999999999997777744221 11 111122221 21
Q ss_pred eEEEeecC--cCCCCCCCChHHHHHHHHhCceEEeeC
Q psy11278 72 IFCFEYPL--MGSTPNANSPFVQIIQEAYNVQVMFRN 106 (238)
Q Consensus 72 ~~~~~~p~--~~~~~~~~g~~i~~i~~~~gv~I~~~~ 106 (238)
.....+|. .+..+|++|.+++-..+-+|-++.+..
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 11122332 233578899999988888887777654
No 123
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.43 E-value=1.3 Score=31.92 Aligned_cols=30 Identities=23% Similarity=0.315 Sum_probs=24.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCE
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCH 31 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~ 31 (238)
++.|-...-|.|||++|++|++|++.....
T Consensus 64 ~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 64 EVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 466777778999999999999999876543
No 124
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.20 E-value=1.6 Score=29.85 Aligned_cols=27 Identities=26% Similarity=0.490 Sum_probs=21.7
Q ss_pred EEEecCCccceeeccCCccHHHHHHHc
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEET 28 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t 28 (238)
++.|-...-|.+||++|.+|++|++..
T Consensus 41 ~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 41 QITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEECCCCceECCCchhHHHHHHHH
Confidence 355666677999999999999988765
No 125
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=79.78 E-value=1.8 Score=38.05 Aligned_cols=38 Identities=13% Similarity=0.115 Sum_probs=34.4
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN 187 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~ 187 (238)
+.+.+|....+.-||++|.+++--+.-||.+|.+-...
T Consensus 305 ~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 305 ARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred EEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 78999999999999999999999999999999875433
No 126
>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=79.00 E-value=11 Score=32.93 Aligned_cols=84 Identities=10% Similarity=0.084 Sum_probs=51.6
Q ss_pred ccceeeccCCccHHHHHHHc-CCEEEecCCCCCC------CCCCCCeEEE--EeCHHHHHHHHHHHHhhCCceEEEeecC
Q psy11278 9 DHSHIIGRGGLTIKKVMEET-GCHVHFPDSNRSV------NAEKSNQVSI--AGSLLGLERARYRVRELTPLIFCFEYPL 79 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t-~~~I~i~~~~~~~------~~~~~~~v~I--~G~~~~v~~A~~~I~~~~~~~~~~~~p~ 79 (238)
-+|..||++|++|+.|.++. |=+|++-.-++.. ......++.| .-. +. .....-+|.
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~fi~nal~Pa~v~~v~i~~~-~~-------------~~~~v~V~~ 309 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVEVLDE-DK-------------HSAEVVVPD 309 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHHHHHHhcCCceEEEEEEEcC-CC-------------cEEEEEECh
Confidence 46999999999999999998 8888885533210 0000111111 110 00 012223332
Q ss_pred --cCCCCCCCChHHHHHHHHhCceEEeeC
Q psy11278 80 --MGSTPNANSPFVQIIQEAYNVQVMFRN 106 (238)
Q Consensus 80 --~~~~~~~~g~~i~~i~~~~gv~I~~~~ 106 (238)
.+..+|++|.+++-..+-+|.+|.+.+
T Consensus 310 ~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 310 DQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred HHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 233578999999998888899988764
No 127
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=78.01 E-value=1.9 Score=39.40 Aligned_cols=36 Identities=17% Similarity=0.156 Sum_probs=33.6
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
+.+.+|....+.-|||+|++++..++-||.+|.+-.
T Consensus 304 ~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 304 ADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 788999999999999999999999999999998754
No 128
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=77.83 E-value=6.3 Score=34.33 Aligned_cols=50 Identities=12% Similarity=0.081 Sum_probs=43.9
Q ss_pred CCccceeeccCCccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHH
Q psy11278 7 YTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVR 66 (238)
Q Consensus 7 ~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 66 (238)
....-.+.|..|.+++.|++.+|+.|.... +.+.|.|....|+.|...+.
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARG----------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCC----------ceEEEEechHHHHHHHHHHh
Confidence 345678999999999999999999998865 68999999879999999886
No 129
>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=77.45 E-value=3.2 Score=31.44 Aligned_cols=34 Identities=24% Similarity=0.434 Sum_probs=28.7
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD 36 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~ 36 (238)
+.|-...=|.+||++|.++++|..+||-+-.+-.
T Consensus 80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 4455666799999999999999999998887754
No 130
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=76.58 E-value=2.5 Score=34.66 Aligned_cols=28 Identities=21% Similarity=0.411 Sum_probs=23.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETG 29 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~ 29 (238)
++.|-...=|.+||++|++|++|++...
T Consensus 54 ~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 54 RVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred EEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 4566677779999999999999988654
No 131
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=75.74 E-value=6.1 Score=34.39 Aligned_cols=54 Identities=22% Similarity=0.239 Sum_probs=45.9
Q ss_pred CCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHH--hhc
Q psy11278 155 SPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV--VSS 219 (238)
Q Consensus 155 ~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~--~~l 219 (238)
+....-.+.|..|.+++.++...|+.|... .+.++|+|....|..|.+.+. .++
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r-----------G~~~~i~g~~~~v~~A~~~l~~l~~~ 77 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR-----------GEAVRIIGARPLVDVATRVLLTLELL 77 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC-----------CceEEEEechHHHHHHHHHHhHHHHH
Confidence 345667889999999999999999999865 368999999879999999888 554
No 132
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=74.05 E-value=2.9 Score=37.64 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=33.5
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPE 185 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~ 185 (238)
+.+.+|....+.-|||+|++++--+.-||.+|.+-.
T Consensus 337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 337 AHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 788999999999999999999999999999998754
No 133
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=73.40 E-value=4 Score=31.79 Aligned_cols=36 Identities=14% Similarity=0.185 Sum_probs=28.9
Q ss_pred EEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278 151 MMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN 187 (238)
Q Consensus 151 ~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~ 187 (238)
-+.+.+.. |.-||++|.+++.+++..|-+|.+-..+
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 34455556 8899999999999999999998775543
No 134
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=72.16 E-value=19 Score=34.26 Aligned_cols=112 Identities=18% Similarity=0.201 Sum_probs=66.8
Q ss_pred HHHHHHhhCCce-----EEEeecCcCC---C---CCCCChHHHHHHHHhCceEEeeCCCCCCCcEEEEEccccchHHHHH
Q psy11278 61 ARYRVRELTPLI-----FCFEYPLMGS---T---PNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKE 129 (238)
Q Consensus 61 A~~~I~~~~~~~-----~~~~~p~~~~---~---~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ 129 (238)
.++.|.+.+|.. ..|+=|.+.. . ...++..++++.++.--+|.+.+.|. +.-+ -+.|++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~egp~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~-------~~~~---~~~~~~ 73 (630)
T TIGR03675 4 IKEIINELLPKDIKITDVEFEGPELVIYTKNPELFAKDDDLVKELAKKLRKRIVIRPDPS-------VLLP---PEEAIE 73 (630)
T ss_pred HHHHHHHhCCCCCeEEEEEEeCCeEEEEeCCHHHhccchHHHHHHHHHhhceEEEecChh-------hcCC---HHHHHH
Confidence 355666776632 3444454221 1 12467889999888877777765332 1112 234555
Q ss_pred HHHHHHHHhhcccccc--ceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278 130 ATTKLIEHMCGSLANQ--TSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 130 ai~~~~~~~~~~~~~~--~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~ 183 (238)
.|.+++..-+ ...+- ...+-+|.|-+..-|.+||++|.++++|.++||-+-.+
T Consensus 74 ~i~~~~~~~~-~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~ 128 (630)
T TIGR03675 74 KIKEIVPEEA-GITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKV 128 (630)
T ss_pred HHHHhCCCcC-CceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeE
Confidence 5555443111 11110 01135677777888999999999999999999988554
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=71.25 E-value=4.3 Score=27.75 Aligned_cols=29 Identities=10% Similarity=0.187 Sum_probs=22.6
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTG 178 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tg 178 (238)
..+.|....-|.+||++|+.|++++..-.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence 45555556778999999999999988753
No 136
>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=69.75 E-value=3.6 Score=29.58 Aligned_cols=31 Identities=10% Similarity=0.170 Sum_probs=25.0
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCe
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQ 180 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~ 180 (238)
..|.|-...-|.+||++|+.|++|+......
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 5666666777999999999999999875554
No 137
>PRK15494 era GTPase Era; Provisional
Probab=62.96 E-value=6.8 Score=34.14 Aligned_cols=24 Identities=29% Similarity=0.415 Sum_probs=18.7
Q ss_pred EEecCC-ccceeeccCCccHHHHHH
Q psy11278 3 LDVSYT-DHSHIIGRGGLTIKKVME 26 (238)
Q Consensus 3 i~ip~~-~~g~IIGk~G~~I~~I~~ 26 (238)
|.|..+ +.+.|||++|+.|++|..
T Consensus 277 i~v~~~sqk~iiiG~~g~~ik~i~~ 301 (339)
T PRK15494 277 IVVSRESYKTIILGKNGSKIKEIGA 301 (339)
T ss_pred EEECCCCceeEEEcCCcHHHHHHHH
Confidence 445555 449999999999999973
No 138
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=60.71 E-value=8.3 Score=31.66 Aligned_cols=28 Identities=11% Similarity=0.207 Sum_probs=22.9
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHh
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQT 177 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~t 177 (238)
..|.|....=|.+||++|+.|++|++..
T Consensus 53 ~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 53 TRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred eEEEEEeCCCcceEcCCCccHHHHHHHH
Confidence 5667766777899999999999988753
No 139
>PRK00089 era GTPase Era; Reviewed
Probab=60.57 E-value=5.4 Score=33.71 Aligned_cols=24 Identities=33% Similarity=0.541 Sum_probs=18.4
Q ss_pred EEecCC-ccceeeccCCccHHHHHH
Q psy11278 3 LDVSYT-DHSHIIGRGGLTIKKVME 26 (238)
Q Consensus 3 i~ip~~-~~g~IIGk~G~~I~~I~~ 26 (238)
+.|..+ +.+.|||++|++|++|..
T Consensus 230 i~v~~~~~k~i~ig~~g~~i~~i~~ 254 (292)
T PRK00089 230 IYVERDSQKGIIIGKGGAMLKKIGT 254 (292)
T ss_pred EEEccCCceeEEEeCCcHHHHHHHH
Confidence 334444 559999999999999984
No 140
>COG1159 Era GTPase [General function prediction only]
Probab=59.09 E-value=6.1 Score=33.68 Aligned_cols=23 Identities=35% Similarity=0.492 Sum_probs=18.5
Q ss_pred EEecCC-ccceeeccCCccHHHHH
Q psy11278 3 LDVSYT-DHSHIIGRGGLTIKKVM 25 (238)
Q Consensus 3 i~ip~~-~~g~IIGk~G~~I~~I~ 25 (238)
+.|+.+ +-+.||||+|++||+|-
T Consensus 233 I~Ver~sQK~IiIGk~G~~iK~IG 256 (298)
T COG1159 233 IYVERESQKGIIIGKNGAMIKKIG 256 (298)
T ss_pred EEEecCCccceEECCCcHHHHHHH
Confidence 445554 55999999999999997
No 141
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=58.86 E-value=15 Score=26.36 Aligned_cols=32 Identities=19% Similarity=0.114 Sum_probs=25.6
Q ss_pred CCCeEEEEeCHHHHHHHHHHHHhhCCceEEEe
Q psy11278 45 KSNQVSIAGSLLGLERARYRVRELTPLIFCFE 76 (238)
Q Consensus 45 ~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~ 76 (238)
.+..+.|+|+..+|+.|.+.+.+.+.....|.
T Consensus 73 FsGslvitGdvs~Ve~Al~~V~~~l~~~L~F~ 104 (111)
T PRK15468 73 FSGALVIYGSVGAVEEALSQTVSGLGRLLNYT 104 (111)
T ss_pred cceeEEEEccHHHHHHHHHHHHHHHHhhcCcc
Confidence 45799999999999999999987766544443
No 142
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=58.72 E-value=8.4 Score=34.00 Aligned_cols=85 Identities=9% Similarity=0.100 Sum_probs=50.8
Q ss_pred ccceeeccCCccHHHHHHHc-CCEEEecCCCCCC------CCCCCCeEEEEe-CHHHHHHHHHHHHhhCCceEEEeecC-
Q psy11278 9 DHSHIIGRGGLTIKKVMEET-GCHVHFPDSNRSV------NAEKSNQVSIAG-SLLGLERARYRVRELTPLIFCFEYPL- 79 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t-~~~I~i~~~~~~~------~~~~~~~v~I~G-~~~~v~~A~~~I~~~~~~~~~~~~p~- 79 (238)
-+|..||++|++|+.|.++. |=+|++-.-++.. ......+..|.= ..+ .....+-+|.
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~fi~nal~Pa~v~~v~i~~~~-------------~~~~~v~V~~~ 312 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFVANALSPAKVVSVEVDDEE-------------EKAARVVVPDY 312 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHHHHHhCCCceEEEEEEEcCC-------------CcEEEEEEChh
Confidence 46999999999999999998 8888885533210 000001111110 000 0012223332
Q ss_pred -cCCCCCCCChHHHHHHHHhCceEEeeC
Q psy11278 80 -MGSTPNANSPFVQIIQEAYNVQVMFRN 106 (238)
Q Consensus 80 -~~~~~~~~g~~i~~i~~~~gv~I~~~~ 106 (238)
.+..+|++|.+++--.+-+|.++.+.+
T Consensus 313 ~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 313 QLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred hcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 233578999999988888888887755
No 143
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=58.33 E-value=16 Score=30.57 Aligned_cols=30 Identities=17% Similarity=0.310 Sum_probs=21.2
Q ss_pred EEEEEEeCCC-eeeEEecCCCchHHHHHHHh
Q psy11278 148 VIMMMEISPQ-HHPIMEGPNAINLKTIMAQT 177 (238)
Q Consensus 148 ~~~~v~i~~~-~~~~iIG~~G~~I~~I~~~t 177 (238)
+.+.+.+... +-+-|||++|+.|++|...+
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 3455566544 44678999999999887654
No 144
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=56.29 E-value=7.4 Score=31.35 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=27.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEEe
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHF 34 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i 34 (238)
.+.|-.+..+.+||+.|.++..||--++.-++-
T Consensus 94 ~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 94 VVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 356677779999999999999999988866654
No 145
>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=55.18 E-value=25 Score=22.39 Aligned_cols=48 Identities=19% Similarity=0.258 Sum_probs=31.4
Q ss_pred CccHHH--HHHHcCCEEEecCCCCC--CCC-----CCCCeEEEEeCHHHHHHHHHHH
Q psy11278 18 GLTIKK--VMEETGCHVHFPDSNRS--VNA-----EKSNQVSIAGSLLGLERARYRV 65 (238)
Q Consensus 18 G~~I~~--I~~~t~~~I~i~~~~~~--~~~-----~~~~~v~I~G~~~~v~~A~~~I 65 (238)
|.+|++ +.+.+++.|---..+.. .|. ...+.+.+.|++++++++.+.+
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~~ 70 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFRELF 70 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHHT
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHhh
Confidence 568888 88888888743222210 111 1346999999999999987653
No 146
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=53.38 E-value=1.1e+02 Score=23.98 Aligned_cols=25 Identities=20% Similarity=0.181 Sum_probs=18.6
Q ss_pred CCCeEEEEe--CHHHHHHHHHHHHhhC
Q psy11278 45 KSNQVSIAG--SLLGLERARYRVRELT 69 (238)
Q Consensus 45 ~~~~v~I~G--~~~~v~~A~~~I~~~~ 69 (238)
.++.+.++| +.+....|.+.+..++
T Consensus 54 ~sGKivitGaks~~~~~~a~~~~~~~L 80 (174)
T cd00652 54 SSGKMVITGAKSEEDAKLAARKYARIL 80 (174)
T ss_pred CCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 457999999 5788888877775543
No 147
>PRK15494 era GTPase Era; Provisional
Probab=53.35 E-value=21 Score=31.08 Aligned_cols=28 Identities=25% Similarity=0.315 Sum_probs=20.5
Q ss_pred EEEEEeCCC-eeeEEecCCCchHHHHHHH
Q psy11278 149 IMMMEISPQ-HHPIMEGPNAINLKTIMAQ 176 (238)
Q Consensus 149 ~~~v~i~~~-~~~~iIG~~G~~I~~I~~~ 176 (238)
.+.+.+... +-+-|||++|+.|++|...
T Consensus 274 ~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 274 NQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 355666555 4467899999999987654
No 148
>PRK00089 era GTPase Era; Reviewed
Probab=53.31 E-value=21 Score=30.06 Aligned_cols=29 Identities=17% Similarity=0.205 Sum_probs=20.3
Q ss_pred EEEEEeCCC-eeeEEecCCCchHHHHHHHh
Q psy11278 149 IMMMEISPQ-HHPIMEGPNAINLKTIMAQT 177 (238)
Q Consensus 149 ~~~v~i~~~-~~~~iIG~~G~~I~~I~~~t 177 (238)
.+.+.+... +-+-|||++|+.|++|...+
T Consensus 227 ~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 227 EATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 355555444 44678999999999876543
No 149
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=52.27 E-value=13 Score=34.24 Aligned_cols=34 Identities=24% Similarity=0.441 Sum_probs=28.1
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD 36 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~ 36 (238)
+.|-++.=|.+|||+|++.+.|.++||-.-.+-.
T Consensus 103 ViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 103 VIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred EEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 4556667799999999999999999997766644
No 150
>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=51.25 E-value=45 Score=25.90 Aligned_cols=41 Identities=17% Similarity=0.311 Sum_probs=34.0
Q ss_pred ccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278 19 LTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68 (238)
Q Consensus 19 ~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 68 (238)
..+++|.+-.|+-+.+ + +...|.|.|+.+.|..|.+.+..+
T Consensus 126 erl~ei~E~~gvI~Ef-e--------e~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 126 ERLQEISEWHGVIFEF-E--------EDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred HHHHHHHHHhceeEEe-c--------CCcEEEEeccHHHHHHHHHHHHHH
Confidence 4678888888999988 2 246899999999999999988654
No 151
>COG4810 EutS Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=50.47 E-value=23 Score=24.98 Aligned_cols=34 Identities=18% Similarity=0.120 Sum_probs=26.9
Q ss_pred CCCeEEEEeCHHHHHHHHHHHHhhCCceEEEeec
Q psy11278 45 KSNQVSIAGSLLGLERARYRVRELTPLIFCFEYP 78 (238)
Q Consensus 45 ~~~~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p 78 (238)
.+..+.++|+..+|+.|.+++...+.+...|.++
T Consensus 83 FsGalvltGdv~aVE~aLkqv~~~L~e~l~ft~c 116 (121)
T COG4810 83 FSGALVLTGDVGAVEEALKQVVSGLGELLNFTLC 116 (121)
T ss_pred ccceEEEEcchHHHHHHHHHHHHHHHHHhceeee
Confidence 4578999999999999999997776665555554
No 152
>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=50.44 E-value=14 Score=29.57 Aligned_cols=29 Identities=28% Similarity=0.396 Sum_probs=23.5
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGC 30 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~ 30 (238)
++.|-...-|.+||++|.+|++|.++..-
T Consensus 41 ~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 41 KVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred EEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 45666777799999999999999887643
No 153
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=49.71 E-value=22 Score=28.70 Aligned_cols=34 Identities=9% Similarity=0.096 Sum_probs=29.9
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEc
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF 183 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~ 183 (238)
..+.|.....+.+||+.|.+++.|+--+++.++-
T Consensus 93 v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 93 VVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 6778888889999999999999999998887664
No 154
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=49.48 E-value=16 Score=29.52 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=23.4
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCE
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCH 31 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~ 31 (238)
.+.|-...-|.+||++|++|+++++...-.
T Consensus 43 ~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 43 RITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 345556677999999999999999876543
No 155
>CHL00048 rps3 ribosomal protein S3
Probab=49.24 E-value=16 Score=29.74 Aligned_cols=29 Identities=14% Similarity=0.043 Sum_probs=23.3
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGC 30 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~ 30 (238)
++.|-...-+.+||++|.+|++|++...-
T Consensus 69 ~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k 97 (214)
T CHL00048 69 QVIIYTGFPKLLIERKGRGIEELQINLQK 97 (214)
T ss_pred EEEEEECCCceEECCCcHhHHHHHHHHHH
Confidence 45566667789999999999999987643
No 156
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=49.00 E-value=1.6e+02 Score=27.66 Aligned_cols=111 Identities=16% Similarity=0.124 Sum_probs=62.2
Q ss_pred CccHHHHHHHcCCEEEecC--CCC----CCCC---CCCCeEEEEeCHHHHHHHHHHHHhhCCc------eEEEeecCcCC
Q psy11278 18 GLTIKKVMEETGCHVHFPD--SNR----SVNA---EKSNQVSIAGSLLGLERARYRVRELTPL------IFCFEYPLMGS 82 (238)
Q Consensus 18 G~~I~~I~~~t~~~I~i~~--~~~----~~~~---~~~~~v~I~G~~~~v~~A~~~I~~~~~~------~~~~~~p~~~~ 82 (238)
|.++.++...+...+.+.. .++ ..++ ...+.+.+.|+.++++++.+.+-.-... ....+. .+.+
T Consensus 232 GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~~~~~~~~~~~~~e~-VV~~ 310 (562)
T TIGR03802 232 GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEVQEVEGLDVPMETKD-VVLT 310 (562)
T ss_pred CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCccCCccccCCceEEEE-EEEC
Confidence 6789999876643332211 111 0011 2347999999999999888775322110 000111 0111
Q ss_pred CCCCCChHHHHHH-H-----HhCceEEeeCC--------CC---CCCcEEEEEccccchHHHHH
Q psy11278 83 TPNANSPFVQIIQ-E-----AYNVQVMFRNR--------PK---LQPTLVMVKGCEKDVERVKE 129 (238)
Q Consensus 83 ~~~~~g~~i~~i~-~-----~~gv~I~~~~~--------~~---~~~~~v~I~G~~~~v~~a~~ 129 (238)
.....|++++++. + .||+.+.--.+ ++ ..++.+.+.|++++++++.+
T Consensus 311 ~S~liGkTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~ 374 (562)
T TIGR03802 311 NKEYNGKTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAK 374 (562)
T ss_pred CcccCCccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHH
Confidence 2233588899886 2 67887753221 11 13589999999888777553
No 157
>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=48.49 E-value=48 Score=21.22 Aligned_cols=21 Identities=24% Similarity=0.245 Sum_probs=18.0
Q ss_pred CeEEEEeCHHHHHHHHHHHHh
Q psy11278 47 NQVSIAGSLLGLERARYRVRE 67 (238)
Q Consensus 47 ~~v~I~G~~~~v~~A~~~I~~ 67 (238)
..+.|.|+.++|+.|.+.+++
T Consensus 39 ~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 39 ITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred EEEEEEecHHHHHHHHHHHhh
Confidence 467789999999999998854
No 158
>COG1159 Era GTPase [General function prediction only]
Probab=48.22 E-value=25 Score=30.06 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=20.1
Q ss_pred EEEEEeCCC-eeeEEecCCCchHHHHHHH
Q psy11278 149 IMMMEISPQ-HHPIMEGPNAINLKTIMAQ 176 (238)
Q Consensus 149 ~~~v~i~~~-~~~~iIG~~G~~I~~I~~~ 176 (238)
.+.+.++.. +=+-|||++|+.|++|-..
T Consensus 230 ~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 230 HATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 345566554 4567999999999987554
No 159
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=47.37 E-value=17 Score=29.70 Aligned_cols=32 Identities=13% Similarity=0.200 Sum_probs=25.1
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcCCEEE
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVH 33 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~ 33 (238)
++.|-...-|.+||++|..|++|+++..-.+.
T Consensus 47 ~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~ 78 (220)
T PTZ00084 47 EIIIRATRTREVLGDKGRRIRELTSLLQKRFG 78 (220)
T ss_pred EEEEEECCCccEEcCCchHHHHHHHHHHHHhC
Confidence 45666677799999999999999987754443
No 160
>KOG1423|consensus
Probab=46.19 E-value=31 Score=29.92 Aligned_cols=32 Identities=6% Similarity=0.147 Sum_probs=24.8
Q ss_pred EEEEEeCCC-eeeEEecCCCchHHHHHHHhCCe
Q psy11278 149 IMMMEISPQ-HHPIMEGPNAINLKTIMAQTGAQ 180 (238)
Q Consensus 149 ~~~v~i~~~-~~~~iIG~~G~~I~~I~~~tga~ 180 (238)
..++.+|.. +...|||++|..|++|-.+.+-.
T Consensus 329 ~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~d 361 (379)
T KOG1423|consen 329 QVEVVCPKNSQKKLLIGKGGKKISQIGTRANED 361 (379)
T ss_pred EEEEEcCCCcceeEEEcCCCccHHHHHHHHHHH
Confidence 356666665 66789999999999998876654
No 161
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=45.15 E-value=31 Score=24.73 Aligned_cols=44 Identities=23% Similarity=0.227 Sum_probs=34.2
Q ss_pred hCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCCCCceEEEEeec
Q psy11278 177 TGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIP 232 (238)
Q Consensus 177 tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~~~p~~~~~~~~ 232 (238)
.++.|-|-+.= ...+.|+|...+|+.|.+.+.+.+ .-.|.|++.
T Consensus 63 a~V~igF~DRF--------sGslvitGdvs~Ve~Al~~V~~~l----~~~L~F~~~ 106 (111)
T PRK15468 63 ADVHIGFLDRF--------SGALVIYGSVGAVEEALSQTVSGL----GRLLNYTLC 106 (111)
T ss_pred cCcEEeeeecc--------ceeEEEEccHHHHHHHHHHHHHHH----HhhcCcccc
Confidence 45566665432 357999999999999999999999 667777765
No 162
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=44.14 E-value=60 Score=24.67 Aligned_cols=41 Identities=17% Similarity=0.310 Sum_probs=33.9
Q ss_pred ccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278 19 LTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68 (238)
Q Consensus 19 ~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 68 (238)
..++.|.+-.|+-|.+.. .+.|.|.|+.+.|-.|.+.|..+
T Consensus 126 eRlqDi~E~hgvIiE~~E---------~D~V~i~Gd~drVk~aLke~~~~ 166 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE---------YDLVAIYGDSDRVKKALKEIGSF 166 (170)
T ss_pred HHHHHHHHhhheeEEeee---------ccEEEEeccHHHHHHHHHHHHHH
Confidence 356777777888888863 36999999999999999999876
No 163
>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=43.07 E-value=74 Score=20.86 Aligned_cols=24 Identities=25% Similarity=0.465 Sum_probs=21.1
Q ss_pred CCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278 45 KSNQVSIAGSLLGLERARYRVREL 68 (238)
Q Consensus 45 ~~~~v~I~G~~~~v~~A~~~I~~~ 68 (238)
..+.+.|.|+++.++..+..|+.+
T Consensus 53 ~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 53 RTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp TTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCEEEEEeCHHHHHHHHHHHHHH
Confidence 347999999999999999999765
No 164
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=41.92 E-value=2.4e+02 Score=26.60 Aligned_cols=122 Identities=15% Similarity=0.167 Sum_probs=63.8
Q ss_pred CChHHHHHHHHh--CceEEe--------eCCCCC---CCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEE
Q psy11278 87 NSPFVQIIQEAY--NVQVMF--------RNRPKL---QPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMME 153 (238)
Q Consensus 87 ~g~~i~~i~~~~--gv~I~~--------~~~~~~---~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~ 153 (238)
.|.++.++...+ ++.+.- .+.|+. ..+.+.+.|.+++++++.+.+..-.... ........ ...+.
T Consensus 231 iGkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~~~~-~~~~~~~~-~e~VV 308 (562)
T TIGR03802 231 IGKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEVQEV-EGLDVPME-TKDVV 308 (562)
T ss_pred CCCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCccCCc-cccCCceE-EEEEE
Confidence 377888887654 554421 111111 3589999999887766543321100000 00000111 12222
Q ss_pred eCCCeeeEEecCCCchHHHHH------HHhCCeEE-ccCCC-----CCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278 154 ISPQHHPIMEGPNAINLKTIM------AQTGAQIV-FPEAN-----DPIIPVLKKSSVTVSGNIDSVYLARQMLV 216 (238)
Q Consensus 154 i~~~~~~~iIG~~G~~I~~I~------~~tga~I~-~p~~~-----~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 216 (238)
+| .+.++ |.+++++. +..|+.|. +-+.+ .++..-...+.+.+.|++++++++.+.+-
T Consensus 309 ~~---~S~li---GkTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 309 LT---NKEYN---GKTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EC---CcccC---CccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcC
Confidence 22 13344 45888887 26788752 22211 12212234689999999999999877644
No 165
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=40.89 E-value=1.7e+02 Score=22.65 Aligned_cols=78 Identities=8% Similarity=0.165 Sum_probs=50.1
Q ss_pred eEEEEeCHHHHHHHHHHHHhhCCceEEEeec---CcC-------C-CCCCCChHHHHHHHHhCceEEeeCCCCCCCcEEE
Q psy11278 48 QVSIAGSLLGLERARYRVRELTPLIFCFEYP---LMG-------S-TPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVM 116 (238)
Q Consensus 48 ~v~I~G~~~~v~~A~~~I~~~~~~~~~~~~p---~~~-------~-~~~~~g~~i~~i~~~~gv~I~~~~~~~~~~~~v~ 116 (238)
.+.+.|+.+.+++..+++.++.+...-.++. .+. . ........+.++.+.|++++.=-.. .+-.+.
T Consensus 47 ti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~LiKv~~~~~~r~~i~~i~~~f~a~ivdv~~---~~~~iE 123 (161)
T PRK11895 47 TIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELALVKVRASGENRAEILRLADIFRAKIVDVTP---ESLTIE 123 (161)
T ss_pred EEEEECCHHHHHHHHHHHhccccEEEEEecCCcchhheEEEEEEEECCcccHHHHHHHHHHhCCEEEEecC---CEEEEE
Confidence 4666799999999999999988754333321 100 0 1112345677888889888753321 246789
Q ss_pred EEccccchHHHH
Q psy11278 117 VKGCEKDVERVK 128 (238)
Q Consensus 117 I~G~~~~v~~a~ 128 (238)
++|.++.+++..
T Consensus 124 ~tG~~~ki~~~~ 135 (161)
T PRK11895 124 VTGDSDKIDAFI 135 (161)
T ss_pred EeCCHHHHHHHH
Confidence 999987665544
No 166
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=40.71 E-value=1.8e+02 Score=22.82 Aligned_cols=25 Identities=16% Similarity=0.094 Sum_probs=18.0
Q ss_pred CCCeEEEEe--CHHHHHHHHHHHHhhC
Q psy11278 45 KSNQVSIAG--SLLGLERARYRVRELT 69 (238)
Q Consensus 45 ~~~~v~I~G--~~~~v~~A~~~I~~~~ 69 (238)
.++.+.++| +.+.+..|.+.+..++
T Consensus 54 ~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 54 SSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 357899999 5677887777775543
No 167
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.29 E-value=77 Score=24.08 Aligned_cols=41 Identities=27% Similarity=0.251 Sum_probs=34.6
Q ss_pred chHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 168 INLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 168 ~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
.++..|.+..|+-|-+.. .+.|.|.|..+-|.+|.+.|..+
T Consensus 126 eRlqDi~E~hgvIiE~~E----------~D~V~i~Gd~drVk~aLke~~~~ 166 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE----------YDLVAIYGDSDRVKKALKEIGSF 166 (170)
T ss_pred HHHHHHHHhhheeEEeee----------ccEEEEeccHHHHHHHHHHHHHH
Confidence 467788888898888763 47999999999999999988765
No 168
>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=39.80 E-value=32 Score=32.80 Aligned_cols=34 Identities=24% Similarity=0.435 Sum_probs=28.9
Q ss_pred EEecCCccceeeccCCccHHHHHHHcCCEEEecC
Q psy11278 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPD 36 (238)
Q Consensus 3 i~ip~~~~g~IIGk~G~~I~~I~~~t~~~I~i~~ 36 (238)
+.|-.+.=|.+|||+|+++++|-++||-+-.+-.
T Consensus 97 v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 97 VIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred EEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 4555667799999999999999999998888755
No 169
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=39.51 E-value=71 Score=21.12 Aligned_cols=44 Identities=11% Similarity=0.068 Sum_probs=31.3
Q ss_pred CchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 167 AINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 167 G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
-..|.+|.+.++|+|.=-.+ +.-.+.++|+++.+....+++..+
T Consensus 16 r~ei~~l~~~f~a~ivd~~~--------~~~iie~tG~~~kid~fi~~l~~~ 59 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVSP--------DSIIIELTGTPEKIDAFIKLLKPF 59 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEET--------TEEEEEEEE-HHHHHHHHHHSTGG
T ss_pred HHHHHHHHHHhCCEEEEECC--------CEEEEEEcCCHHHHHHHHHHhhhc
Confidence 45788899999999643222 258999999999999877776653
No 170
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=38.75 E-value=1.6e+02 Score=22.72 Aligned_cols=110 Identities=16% Similarity=0.208 Sum_probs=62.1
Q ss_pred HHHHHHhCceEE-eeCCCC--CCC--cEEEEEccccchHHHHHHHHHHHHHhhc-cccccceE-----EEEEEeCCCeee
Q psy11278 92 QIIQEAYNVQVM-FRNRPK--LQP--TLVMVKGCEKDVERVKEATTKLIEHMCG-SLANQTSV-----IMMMEISPQHHP 160 (238)
Q Consensus 92 ~~i~~~~gv~I~-~~~~~~--~~~--~~v~I~G~~~~v~~a~~ai~~~~~~~~~-~~~~~~~~-----~~~v~i~~~~~~ 160 (238)
..+-...|.+|. +.-.|. ... -.+++.|+.+.+++..+.+.++++-..- .+.+...+ -..+..+.
T Consensus 20 ~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~~~~~~i~qi~kQl~KLidV~~V~~~~~~~~v~rEl~LiKv~~~~---- 95 (161)
T PRK11895 20 AGLFSRRGYNIESLTVGPTEDPGLSRMTIVTSGDEQVIEQITKQLNKLIDVLKVVDLTEEAHVERELALVKVRASG---- 95 (161)
T ss_pred HHHHHhCCCcEEEEEeeecCCCCEEEEEEEEECCHHHHHHHHHHHhccccEEEEEecCCcchhheEEEEEEEECCc----
Confidence 344446677763 221121 111 2466778877777777666655542211 11111011 12222211
Q ss_pred EEecCCCchHHHHHHHhCCeEE-ccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 161 IMEGPNAINLKTIMAQTGAQIV-FPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 161 ~iIG~~G~~I~~I~~~tga~I~-~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
.....|-+|.+.++|+|. +.+ +.-.+.++|+++.+..-.+++..+
T Consensus 96 ----~~r~~i~~i~~~f~a~ivdv~~---------~~~~iE~tG~~~ki~~~~~~l~~~ 141 (161)
T PRK11895 96 ----ENRAEILRLADIFRAKIVDVTP---------ESLTIEVTGDSDKIDAFIDLLRPY 141 (161)
T ss_pred ----ccHHHHHHHHHHhCCEEEEecC---------CEEEEEEeCCHHHHHHHHHHhhhc
Confidence 134678899999999964 432 257999999999999877777665
No 171
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=38.68 E-value=31 Score=27.87 Aligned_cols=30 Identities=10% Similarity=0.169 Sum_probs=23.0
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGA 179 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga 179 (238)
..+.|....-+.+||++|++|++++....-
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 445555566789999999999999887544
No 172
>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=38.68 E-value=95 Score=24.17 Aligned_cols=41 Identities=17% Similarity=0.234 Sum_probs=33.7
Q ss_pred chHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 168 INLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 168 ~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
..+.+|++-.|+-+-+. + ...|.|-|..+.|..|.+.+..+
T Consensus 126 erl~ei~E~~gvI~Efe---e-------~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 126 ERLQEISEWHGVIFEFE---E-------DDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred HHHHHHHHHhceeEEec---C-------CcEEEEeccHHHHHHHHHHHHHH
Confidence 46789999999999981 1 36799999999999999877543
No 173
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=38.09 E-value=2e+02 Score=22.60 Aligned_cols=94 Identities=15% Similarity=0.170 Sum_probs=53.9
Q ss_pred EEEEEccccchHHHHHHHHHHHHHhhcc-ccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCCCCCCC
Q psy11278 114 LVMVKGCEKDVERVKEATTKLIEHMCGS-LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIP 192 (238)
Q Consensus 114 ~v~I~G~~~~v~~a~~ai~~~~~~~~~~-~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~ 192 (238)
.+.+.|..+..+...+.+.++.+-..-. +.+...+.-++.+=+-. .=..+...+.++.+.++|+|.=-..
T Consensus 47 TIvv~~~~~~ieqL~kQL~KLidVl~V~~~~~~~~v~rEl~LiKv~---~~~~~r~ei~~~~~~f~a~ivdv~~------ 117 (174)
T CHL00100 47 TMVVPGDDRTIEQLTKQLYKLVNILKVQDITNIPCVERELMLIKIN---VNSQTRPEILEIAQIFRAKVVDLSE------ 117 (174)
T ss_pred EEEEECCHHHHHHHHHHHHHHhHhhEEEecCCccceeeEEEEEEEe---cCCcCHHHHHHHHHHhCCEEEEecC------
Confidence 4666666445667776766666643211 11111111111110000 0123456788999999999743222
Q ss_pred CCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 193 VLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 193 ~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
+.-.+.++|+++.+.....++..+
T Consensus 118 --~~~~ie~tG~~~ki~a~~~~l~~~ 141 (174)
T CHL00100 118 --ESLILEVTGDPGKIVAIEQLLEKF 141 (174)
T ss_pred --CEEEEEEcCCHHHHHHHHHHhhhc
Confidence 247899999999999888777654
No 174
>CHL00048 rps3 ribosomal protein S3
Probab=38.03 E-value=32 Score=27.97 Aligned_cols=29 Identities=3% Similarity=0.044 Sum_probs=23.4
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTG 178 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tg 178 (238)
..+.|-...-+.+||++|..|+++++.-.
T Consensus 68 ~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 68 IQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred EEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 56666666678999999999999998764
No 175
>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=37.86 E-value=33 Score=27.46 Aligned_cols=29 Identities=7% Similarity=0.129 Sum_probs=23.3
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTG 178 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tg 178 (238)
.++.|....-+.+||++|..|+++++.-.
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~ 68 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQ 68 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHH
Confidence 56666666778999999999999887643
No 176
>PLN00062 TATA-box-binding protein; Provisional
Probab=37.39 E-value=2e+02 Score=22.60 Aligned_cols=25 Identities=16% Similarity=0.116 Sum_probs=18.2
Q ss_pred CCCeEEEEe--CHHHHHHHHHHHHhhC
Q psy11278 45 KSNQVSIAG--SLLGLERARYRVRELT 69 (238)
Q Consensus 45 ~~~~v~I~G--~~~~v~~A~~~I~~~~ 69 (238)
.++.+.++| +.+.+..|.+.+..++
T Consensus 54 ~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 54 ASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred CCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 457999999 5678887777775543
No 177
>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=37.00 E-value=1e+02 Score=20.96 Aligned_cols=54 Identities=7% Similarity=0.046 Sum_probs=39.9
Q ss_pred CCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcC
Q psy11278 166 NAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSV 220 (238)
Q Consensus 166 ~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~ 220 (238)
+-..+.++-+..|+.+.+...+... -..++..+++.|+..++..|.+.+..+|+
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~-v~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDR-VEPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-E-EETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCC-ccCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 4467788888899988765433111 11246899999999999999999998873
No 178
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.97 E-value=34 Score=27.98 Aligned_cols=30 Identities=7% Similarity=0.072 Sum_probs=23.4
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHhCC
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQTGA 179 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~tga 179 (238)
.+|.|-...-+.+||++|..|+++++.-.-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k 75 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQK 75 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHH
Confidence 566666666789999999999998876543
No 179
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=34.34 E-value=34 Score=27.77 Aligned_cols=28 Identities=18% Similarity=0.391 Sum_probs=22.3
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETG 29 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~ 29 (238)
++.|-...-+.+||++|.++++|++...
T Consensus 65 ~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 65 RVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred EEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 4556666778999999999999987653
No 180
>PRK03818 putative transporter; Validated
Probab=33.94 E-value=3.3e+02 Score=25.58 Aligned_cols=123 Identities=11% Similarity=0.126 Sum_probs=63.6
Q ss_pred CChHHHHHHHHhC--ceEE-e-------eCCCCC---CCcEEEEEccccchHHHHHHHHHHHHHhhccccccceEEEEEE
Q psy11278 87 NSPFVQIIQEAYN--VQVM-F-------RNRPKL---QPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMME 153 (238)
Q Consensus 87 ~g~~i~~i~~~~g--v~I~-~-------~~~~~~---~~~~v~I~G~~~~v~~a~~ai~~~~~~~~~~~~~~~~~~~~v~ 153 (238)
-|++++++..... +.+. + .+.++. ..+.+.+.|.+++++++.+....-.+. ..+..++. ...+.-
T Consensus 217 iGkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~~-~~~~~~~~-~~~E~V 294 (552)
T PRK03818 217 HGKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVDT-SLSTRGTD-LRSERV 294 (552)
T ss_pred CCCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccCc-cccccCcc-eEEEEE
Confidence 3778888877653 3331 1 011111 358999999988766655332111000 00000111 113333
Q ss_pred eCCCeeeEEecCCCchHHHH--HHHhCCeE-EccCCC-----CCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278 154 ISPQHHPIMEGPNAINLKTI--MAQTGAQI-VFPEAN-----DPIIPVLKKSSVTVSGNIDSVYLARQMLV 216 (238)
Q Consensus 154 i~~~~~~~iIG~~G~~I~~I--~~~tga~I-~~p~~~-----~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 216 (238)
++++ +.++|+ +++++ ++..|+.| .+-+.+ .++..-...+.+.+.|++++++++.+.+.
T Consensus 295 vv~~--S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 295 VVTN--EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAVANVLG 360 (552)
T ss_pred EEcC--hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHHHHHhC
Confidence 3322 345554 77777 46678765 221111 11212234689999999999999877544
No 181
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=33.74 E-value=67 Score=27.71 Aligned_cols=55 Identities=24% Similarity=0.330 Sum_probs=42.2
Q ss_pred ccceeeccCCccHHHHHHHcCCE--EEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhC
Q psy11278 9 DHSHIIGRGGLTIKKVMEETGCH--VHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELT 69 (238)
Q Consensus 9 ~~g~IIGk~G~~I~~I~~~t~~~--I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~ 69 (238)
-+..++|---+.|+++.++.+-. +.+...|. ..++.|+|.++++++|...+++.-
T Consensus 132 ~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N~------~~QiVIsG~~~ale~a~~~~~~~g 188 (310)
T COG0331 132 GMAAVLGLDDEQVEKACEEAAQGTVVEIANYNS------PGQIVISGTKEALEKAAEILKEAG 188 (310)
T ss_pred cHHHHcCCCHHHHHHHHHHhccCCeEEEeeeCC------CCcEEEECCHHHHHHHHHHHHHhh
Confidence 34566777778888888888653 66655443 479999999999999999997664
No 182
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=33.39 E-value=80 Score=27.25 Aligned_cols=68 Identities=10% Similarity=0.124 Sum_probs=49.3
Q ss_pred CeeeEEecCCCchHHHHHHHhCCe--EEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhhcCC---CCceEEEEee
Q psy11278 157 QHHPIMEGPNAINLKTIMAQTGAQ--IVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVR---PRRRLLLITI 231 (238)
Q Consensus 157 ~~~~~iIG~~G~~I~~I~~~tga~--I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~l~~---~~p~~~~~~~ 231 (238)
.-...++|-.-+.|.++.++.+-. |.+-+.+. ...+.|+|.++++++|...+.+.=.+ +.+++.-|+-
T Consensus 131 g~Maav~gl~~e~v~~~~~~~~~~~~v~iaN~N~-------~~QiVIsG~~~ale~a~~~~~~~g~kr~i~l~vs~pfHs 203 (310)
T COG0331 131 GGMAAVLGLDDEQVEKACEEAAQGTVVEIANYNS-------PGQIVISGTKEALEKAAEILKEAGAKRAIPLPVSGPFHS 203 (310)
T ss_pred ccHHHHcCCCHHHHHHHHHHhccCCeEEEeeeCC-------CCcEEEECCHHHHHHHHHHHHHhhhhhhcccCCCchhhh
Confidence 445678888999999999998764 44444443 37899999999999998888776622 3445555543
No 183
>PRK03818 putative transporter; Validated
Probab=32.40 E-value=4.3e+02 Score=24.83 Aligned_cols=111 Identities=16% Similarity=0.181 Sum_probs=63.2
Q ss_pred CccHHHHHHHcCCEEEecC--CCCC--C--C---CCCCCeEEEEeCHHHHHHHHHHHHhhCC-------ceEEEeecCcC
Q psy11278 18 GLTIKKVMEETGCHVHFPD--SNRS--V--N---AEKSNQVSIAGSLLGLERARYRVRELTP-------LIFCFEYPLMG 81 (238)
Q Consensus 18 G~~I~~I~~~t~~~I~i~~--~~~~--~--~---~~~~~~v~I~G~~~~v~~A~~~I~~~~~-------~~~~~~~p~~~ 81 (238)
|.+++++.......+.+.. .+.. . + -...+.+.+.|..++++++...+-.-.. .....+. .+.
T Consensus 218 GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~~~~~~~~~~~~~E~-Vvv 296 (552)
T PRK03818 218 GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVDTSLSTRGTDLRSER-VVV 296 (552)
T ss_pred CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccCccccccCcceEEEE-EEE
Confidence 6799999988765554422 1110 0 1 1234799999999999988877632211 0011110 000
Q ss_pred CCCCCCChHHHHH--HHHhCceEEeeC--------CCCC---CCcEEEEEccccchHHHHH
Q psy11278 82 STPNANSPFVQII--QEAYNVQVMFRN--------RPKL---QPTLVMVKGCEKDVERVKE 129 (238)
Q Consensus 82 ~~~~~~g~~i~~i--~~~~gv~I~~~~--------~~~~---~~~~v~I~G~~~~v~~a~~ 129 (238)
+.....|++++++ ++.||+.+.--. .++. .++.+.+.|++++++++.+
T Consensus 297 ~~S~liGkTL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~ 357 (552)
T PRK03818 297 TNEKVLGKKLRDLHLKNKYGVVISRLNRAGVELVASPDLSLQFGDILNLVGRPEAIDAVAN 357 (552)
T ss_pred cChhccCCcHHHhcccccCCeEEEEEeECCeecCCCCCCEEecCCEEEEEECHHHHHHHHH
Confidence 1122347788876 566888764211 1111 2589999999888777654
No 184
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=31.11 E-value=60 Score=25.17 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=30.6
Q ss_pred HHHHHhCCeEE-ccCC------CCCCCCCCcceEEEEEcCHHHHHHHHHHHH
Q psy11278 172 TIMAQTGAQIV-FPEA------NDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216 (238)
Q Consensus 172 ~I~~~tga~I~-~p~~------~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 216 (238)
+++++|||.|. +-++ ..|...-...+.+.+.|....+..++....
T Consensus 107 ~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 107 NIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred ccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 67899999863 2111 122223345789999999999998887653
No 185
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=28.39 E-value=2.9e+02 Score=21.59 Aligned_cols=24 Identities=25% Similarity=0.346 Sum_probs=17.8
Q ss_pred CCCeEEEEeC--HHHHHHHHHHHHhh
Q psy11278 45 KSNQVSIAGS--LLGLERARYRVREL 68 (238)
Q Consensus 45 ~~~~v~I~G~--~~~v~~A~~~I~~~ 68 (238)
.++.+.++|. .+....|.+.+.++
T Consensus 54 ~sGKiviTGaks~~~~~~a~~~~~~~ 79 (174)
T cd04517 54 SSGKITITGATSEEEAKQAARRAARL 79 (174)
T ss_pred CCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 4579999984 68888888777554
No 186
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=27.75 E-value=1e+02 Score=23.88 Aligned_cols=44 Identities=20% Similarity=0.281 Sum_probs=29.2
Q ss_pred HHHHHcCCEEE--------ecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHH
Q psy11278 23 KVMEETGCHVH--------FPDSNRSVNAEKSNQVSIAGSLLGLERARYRVR 66 (238)
Q Consensus 23 ~I~~~t~~~I~--------i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~ 66 (238)
+++++|||.|- ++++.+...-+.-+++.+.|+...+.++.....
T Consensus 107 ~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 107 NIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred ccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 67889999883 222222111124479999999999988887653
No 187
>cd04910 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase
Probab=26.66 E-value=1.9e+02 Score=18.98 Aligned_cols=53 Identities=23% Similarity=0.310 Sum_probs=39.1
Q ss_pred eccCC--ccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhhCCc
Q psy11278 14 IGRGG--LTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPL 71 (238)
Q Consensus 14 IGk~G--~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~~~~ 71 (238)
+|..| ..|-++-.+.++++-.-..|. .+-.+.+.|+...+.++...+++..|.
T Consensus 12 vG~~g~d~~i~~~l~~~~v~ii~K~~nA-----Ntit~yl~~~~k~~~r~~~~Le~~~p~ 66 (71)
T cd04910 12 VGEVGYDLEILELLQRFKVSIIAKDTNA-----NTITHYLAGSLKTIKRLTEDLENRFPN 66 (71)
T ss_pred cCChhHHHHHHHHHHHcCCeEEEEecCC-----CeEEEEEEcCHHHHHHHHHHHHHhCcc
Confidence 45555 456666778899887765443 345788889999999999999877653
No 188
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=26.31 E-value=3e+02 Score=21.13 Aligned_cols=89 Identities=15% Similarity=0.198 Sum_probs=0.0
Q ss_pred EEEEEccccchHHHHHHHHHHHH------HhhccccccceEEEEEEeCCCeeeEEecCCCchHHHHHHHhCCeEEccCCC
Q psy11278 114 LVMVKGCEKDVERVKEATTKLIE------HMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEAN 187 (238)
Q Consensus 114 ~v~I~G~~~~v~~a~~ai~~~~~------~~~~~~~~~~~~~~~v~i~~~~~~~iIG~~G~~I~~I~~~tga~I~~p~~~ 187 (238)
.+++.|+++.++...+.+.++++ .-..+.-...-.-..+..+. .....|.+|.+.++|+|.=-..+
T Consensus 46 ti~V~~d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl~LiKv~~~~--------~~r~~i~~i~~~f~a~ivdv~~~ 117 (157)
T TIGR00119 46 TIVVVGDDKVLEQITKQLNKLVDVIKVSDLTESAIVERELCLVKVSAPG--------EGRDEIIRLTNIFRGRIVDVSPD 117 (157)
T ss_pred EEEEECCHHHHHHHHHHHhcCccEEEEEecCCCcceeeEEEEEEEECCc--------cCHHHHHHHHHHhCCEEEEecCC
Q ss_pred CCCCCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 188 DPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 188 ~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
.-.+.++|+++.+..-.+++..+
T Consensus 118 --------~~~ie~tG~~~ki~~~~~~l~~~ 140 (157)
T TIGR00119 118 --------SYTVEVTGDSDKIDAFLELLRPF 140 (157)
T ss_pred --------EEEEEEcCCHHHHHHHHHHhhhc
No 189
>TIGR03131 malonate_mdcH malonate decarboxylase, epsilon subunit. Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on an ACP subunit of malonate decarboxylase that has an unusual coenzyme A derivative as its prothetic group.
Probab=25.45 E-value=99 Score=25.97 Aligned_cols=49 Identities=10% Similarity=0.247 Sum_probs=35.9
Q ss_pred EEecCCCchHHHHHHHhCCeEEccCCCCCCCCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 161 IMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 161 ~iIG~~G~~I~~I~~~tga~I~~p~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
.+.|..-..+.++..+.++.|..-+ . .+.++|.|+++.+..+...+...
T Consensus 125 av~~~~~~~~~~~l~~~~v~ia~~N--s-------p~~~visG~~~~l~~l~~~l~~~ 173 (295)
T TIGR03131 125 AVLGLDLAAVEALIAKHGVYLAIIN--A-------PDQVVIAGSRAALRAVAELARAA 173 (295)
T ss_pred EEeCCCHHHHHHHHHHcCEEEEEEc--C-------CCCEEEECCHHHHHHHHHHHHhc
Confidence 4567777778888887775554433 2 26799999999999988887653
No 190
>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=24.90 E-value=1.9e+02 Score=20.64 Aligned_cols=50 Identities=8% Similarity=-0.018 Sum_probs=32.0
Q ss_pred HHHHHHHhCCeEEccCCCCCCCCC-----CcceEEEEEc-CHHHHHHHHHHHHhhc
Q psy11278 170 LKTIMAQTGAQIVFPEANDPIIPV-----LKKSSVTVSG-NIDSVYLARQMLVVSS 219 (238)
Q Consensus 170 I~~I~~~tga~I~~p~~~~~~~~~-----~~~~~v~I~G-~~~~v~~A~~~I~~~l 219 (238)
..+=-+.+++.|.|+++--..... ..+-.+.|.| .+..|..|.+...+.+
T Consensus 42 ~DeAtKaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l 97 (103)
T cd07049 42 LDEATKAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFI 97 (103)
T ss_pred hhhhhhhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHH
Confidence 344456677777777654111110 1223445999 8999999999988887
No 191
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=24.80 E-value=66 Score=26.10 Aligned_cols=28 Identities=11% Similarity=0.211 Sum_probs=22.4
Q ss_pred EEEEeCCCeeeEEecCCCchHHHHHHHh
Q psy11278 150 MMMEISPQHHPIMEGPNAINLKTIMAQT 177 (238)
Q Consensus 150 ~~v~i~~~~~~~iIG~~G~~I~~I~~~t 177 (238)
..+.|-...-+.+||++|..++++++.-
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 5566666667899999999999998664
No 192
>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=24.36 E-value=2.2e+02 Score=18.74 Aligned_cols=27 Identities=19% Similarity=0.265 Sum_probs=22.8
Q ss_pred ceEEEEEcCHHHHHHHHHHHHhhcCCC
Q psy11278 196 KSSVTVSGNIDSVYLARQMLVVSSVRP 222 (238)
Q Consensus 196 ~~~v~I~G~~~~v~~A~~~I~~~l~~~ 222 (238)
...+.|+|...+|+.|.....+.....
T Consensus 39 ~~~~~i~G~vs~V~~Av~a~~~~~~~~ 65 (75)
T PF00936_consen 39 KVTVIITGDVSAVKAAVDAAEEAAGKK 65 (75)
T ss_dssp EEEEEEEESHHHHHHHHHHHHHHHHHT
T ss_pred eEEEEEEECHHHHHHHHHHHHHHHhhc
Confidence 578999999999999999888877443
No 193
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=24.26 E-value=57 Score=26.90 Aligned_cols=28 Identities=21% Similarity=0.414 Sum_probs=21.6
Q ss_pred EEEecCCccceeeccCCccHHHHHHHcC
Q psy11278 2 KLDVSYTDHSHIIGRGGLTIKKVMEETG 29 (238)
Q Consensus 2 ~i~ip~~~~g~IIGk~G~~I~~I~~~t~ 29 (238)
+|.|-...-+.+||++|.+|++|++...
T Consensus 65 ~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 65 RVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 3455555668999999999999988764
No 194
>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=24.01 E-value=2e+02 Score=19.48 Aligned_cols=50 Identities=14% Similarity=0.133 Sum_probs=35.2
Q ss_pred ccHHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHHHHHHHHHHhh
Q psy11278 19 LTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68 (238)
Q Consensus 19 ~~I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 68 (238)
.-+.++-+..+++++....+...-...+...+++|+..++..|.+.+..+
T Consensus 34 ~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~ 83 (88)
T PF02749_consen 34 EEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNF 83 (88)
T ss_dssp HHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence 45667777889888887655432122457999999999999988877544
No 195
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=23.09 E-value=1.1e+02 Score=22.14 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=25.5
Q ss_pred eEEEEEcCHHHHHHHHHHHHhhcCCCCceEEEEeec
Q psy11278 197 SSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIP 232 (238)
Q Consensus 197 ~~v~I~G~~~~v~~A~~~I~~~l~~~~p~~~~~~~~ 232 (238)
..+.|+|...+|+.|.....+.+ .-.+.|.+.
T Consensus 74 g~vii~GdvsaV~aAl~a~~~~~----~~~~~f~~~ 105 (110)
T cd07046 74 GALVITGDVSEVESALEAVVDYL----RETLGFTVC 105 (110)
T ss_pred EEEEEEECHHHHHHHHHHHHHHH----hhccCceec
Confidence 46789999999999999998888 555566553
No 196
>cd07045 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carbox
Probab=22.39 E-value=2.6e+02 Score=18.94 Aligned_cols=37 Identities=19% Similarity=0.210 Sum_probs=26.9
Q ss_pred ceEEEEEcCHHHHHHHHHHHHhhcCCCCceEEEEeec
Q psy11278 196 KSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLLITIP 232 (238)
Q Consensus 196 ~~~v~I~G~~~~v~~A~~~I~~~l~~~~p~~~~~~~~ 232 (238)
...+.++|...+|+.|.....+......-+.-++=+|
T Consensus 38 k~~vii~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~ 74 (84)
T cd07045 38 LVTVKITGDVAAVKAAVEAGAAAAERIGELVSSHVIP 74 (84)
T ss_pred EEEEEEEEcHHHHHHHHHHHHHHHhccCcEEEEEEeC
Confidence 5789999999999999988887775533344444444
No 197
>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=21.12 E-value=1.5e+02 Score=19.17 Aligned_cols=53 Identities=9% Similarity=0.040 Sum_probs=35.5
Q ss_pred CCchHHHHHHHhCCeEEccCCCCCC--CCCCcceEEEEEcCHHHHHHHHHHHHhh
Q psy11278 166 NAINLKTIMAQTGAQIVFPEANDPI--IPVLKKSSVTVSGNIDSVYLARQMLVVS 218 (238)
Q Consensus 166 ~G~~I~~I~~~tga~I~~p~~~~~~--~~~~~~~~v~I~G~~~~v~~A~~~I~~~ 218 (238)
...-|.++.+++|..+.+-...-.. ...-+.-.+.+.|+.+++++|..++.+.
T Consensus 15 ~~piis~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~g~~~~~~~a~~~L~~~ 69 (76)
T PF09383_consen 15 QEPIISQLIREFGVDVNILHGNIEEIQGTPFGILILELPGDDEEIEKAIAYLREQ 69 (76)
T ss_dssp SSCHHHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEES-HHHHHHHHHHHHHT
T ss_pred CchHHHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEECCHHHHHHHHHHHHHC
Confidence 4667889999999988664322100 0011346889999999999999999875
No 198
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=20.58 E-value=4.2e+02 Score=20.70 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=17.8
Q ss_pred CcEEEEEccccchHHHHHHHHHHHHH
Q psy11278 112 PTLVMVKGCEKDVERVKEATTKLIEH 137 (238)
Q Consensus 112 ~~~v~I~G~~~~v~~a~~ai~~~~~~ 137 (238)
+..++++|... .+.++.|+..+...
T Consensus 146 SGKvvitGaks-~~~~~~a~~~i~~~ 170 (174)
T cd04518 146 SGKMVITGAKS-EEDAKRAVEKLLSR 170 (174)
T ss_pred CCEEEEEecCC-HHHHHHHHHHHHHH
Confidence 57899999864 56667776666553
No 199
>PF05651 Diacid_rec: Putative sugar diacid recognition; InterPro: IPR008599 This region is found in several proteins characterised as carbohydrate diacid regulators (e.g. P36047 from SWISSPROT). An HTH DNA-binding motif is found at the C terminus of these proteins suggesting that this region includes the sugar recognition region.
Probab=20.31 E-value=2.8e+02 Score=20.64 Aligned_cols=95 Identities=13% Similarity=0.119 Sum_probs=52.4
Q ss_pred HHHHHHHcCCEEEecCCCCCCCCCCCCeEEEEeCHHHH----HHHHHHHHhhCCceEEEeecCcCCCCCCCChHHHHH-H
Q psy11278 21 IKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGL----ERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQII-Q 95 (238)
Q Consensus 21 I~~I~~~t~~~I~i~~~~~~~~~~~~~~v~I~G~~~~v----~~A~~~I~~~~~~~~~~~~p~~~~~~~~~g~~i~~i-~ 95 (238)
+.++++.++-.|+|-+. ...|.-+++++.+ +.|+..|+.-.+...+.+.. .++ .
T Consensus 10 v~~~~~~i~~~inimd~--------~G~IIAStd~~RIG~~HegA~~~i~~~~~~~i~~~~~-------------~~~~g 68 (135)
T PF05651_consen 10 VDEIMEIIGYNINIMDE--------NGIIIASTDPERIGTFHEGAKEVIRTNKEIEITEEDA-------------EQYPG 68 (135)
T ss_pred HHHHHHHcCCCEEEECC--------CcEEEecCChhhcCccCHHHHHHHHcCCcccccHhHH-------------hhccC
Confidence 56788889999999774 3577778888765 44666665442211110100 000 0
Q ss_pred HHhCceEEeeCCCCCCCcEEEEEccccchHHHHHHHHHHHHH
Q psy11278 96 EAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEH 137 (238)
Q Consensus 96 ~~~gv~I~~~~~~~~~~~~v~I~G~~~~v~~a~~ai~~~~~~ 137 (238)
-+-|+++.+... ..--..+-|+|.|+.+......++...+.
T Consensus 69 ~k~GinlPI~~~-g~~iGviGItG~p~eV~~~~~lvk~~~El 109 (135)
T PF05651_consen 69 VKPGINLPIIFN-GEVIGVIGITGEPEEVRPYAQLVKKMAEL 109 (135)
T ss_pred CCcceeeeEEEC-CEEEEEEEEecCHHHHHHHHHHHHHHHHH
Confidence 012333332221 11125789999999887766555554443
Done!