Query 027782
Match_columns 219
No_of_seqs 125 out of 557
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 15:07:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027782.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027782hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1094 Predicted RNA-binding 100.0 3E-60 6.6E-65 402.1 19.2 179 39-218 6-184 (194)
2 KOG3273 Predicted RNA-binding 100.0 1.1E-58 2.3E-63 394.1 15.5 197 23-219 56-252 (252)
3 PRK13763 putative RNA-processi 100.0 1.8E-45 3.8E-50 310.1 18.8 175 41-218 3-177 (180)
4 TIGR03665 arCOG04150 arCOG0415 100.0 1.8E-45 4E-50 307.9 16.8 170 45-218 2-171 (172)
5 KOG2874 rRNA processing protei 100.0 4.4E-38 9.6E-43 278.7 10.9 183 23-211 40-222 (356)
6 KOG1676 K-homology type RNA bi 99.5 3.1E-14 6.7E-19 137.1 11.4 151 39-197 137-299 (600)
7 TIGR03319 YmdA_YtgF conserved 99.2 2.3E-11 5.1E-16 117.3 8.7 63 138-203 210-276 (514)
8 KOG2193 IGF-II mRNA-binding pr 99.2 5.6E-11 1.2E-15 111.5 10.0 142 39-197 409-563 (584)
9 PRK00106 hypothetical protein; 99.2 7E-11 1.5E-15 114.4 8.7 62 138-202 231-296 (535)
10 KOG1676 K-homology type RNA bi 99.2 5.1E-11 1.1E-15 115.1 7.6 145 39-203 228-394 (600)
11 PRK12704 phosphodiesterase; Pr 99.1 3.8E-10 8.3E-15 109.1 8.0 62 138-202 216-281 (520)
12 KOG2191 RNA-binding protein NO 98.8 1.4E-07 3.1E-12 86.5 15.0 153 40-201 38-207 (402)
13 PRK12705 hypothetical protein; 98.7 1.9E-08 4.2E-13 97.1 6.3 62 138-202 204-269 (508)
14 cd02393 PNPase_KH Polynucleoti 98.6 6.1E-08 1.3E-12 68.3 4.7 50 144-193 10-61 (61)
15 PF00013 KH_1: KH domain syndr 98.6 5.5E-08 1.2E-12 67.2 3.7 49 144-192 8-60 (60)
16 KOG2193 IGF-II mRNA-binding pr 98.5 1.9E-07 4E-12 88.1 7.6 135 42-196 200-350 (584)
17 cd02394 vigilin_like_KH K homo 98.5 1.6E-07 3.5E-12 65.3 5.0 49 144-192 8-61 (62)
18 smart00322 KH K homology RNA-b 98.5 4E-07 8.8E-12 62.0 6.0 52 145-196 12-68 (69)
19 cd02395 SF1_like-KH Splicing f 98.4 9.9E-07 2.1E-11 70.4 7.9 56 146-201 16-98 (120)
20 cd02393 PNPase_KH Polynucleoti 98.4 7.7E-07 1.7E-11 62.6 6.3 58 42-104 3-60 (61)
21 cd00105 KH-I K homology RNA-bi 98.4 5.9E-07 1.3E-11 62.0 5.2 49 144-192 8-63 (64)
22 PRK13763 putative RNA-processi 98.3 1.4E-06 3E-11 73.7 5.6 64 51-121 105-168 (180)
23 cd02396 PCBP_like_KH K homolog 98.2 3E-06 6.5E-11 59.9 5.3 50 143-192 7-64 (65)
24 KOG2190 PolyC-binding proteins 98.1 5.7E-05 1.2E-09 73.0 13.3 150 39-198 41-208 (485)
25 PF00013 KH_1: KH domain syndr 98.0 9.7E-06 2.1E-10 55.9 4.5 58 42-104 1-60 (60)
26 cd02394 vigilin_like_KH K homo 97.8 4.1E-05 9E-10 53.0 5.4 57 43-104 2-61 (62)
27 cd02396 PCBP_like_KH K homolog 97.8 3.7E-05 8.1E-10 54.2 5.2 58 42-104 1-64 (65)
28 TIGR03665 arCOG04150 arCOG0415 97.8 3.5E-05 7.6E-10 64.7 5.5 59 144-202 6-69 (172)
29 PF13014 KH_3: KH domain 97.8 3.2E-05 7E-10 50.4 4.1 27 147-173 2-28 (43)
30 cd00105 KH-I K homology RNA-bi 97.8 8.6E-05 1.9E-09 51.0 5.9 57 43-104 2-63 (64)
31 smart00322 KH K homology RNA-b 97.4 0.00088 1.9E-08 45.2 7.1 62 41-107 3-67 (69)
32 TIGR02696 pppGpp_PNP guanosine 97.2 0.00075 1.6E-08 68.0 7.1 67 42-113 579-645 (719)
33 cd02395 SF1_like-KH Splicing f 97.2 0.0015 3.2E-08 52.2 7.4 67 44-114 3-99 (120)
34 PRK08406 transcription elongat 97.1 0.0011 2.3E-08 54.3 5.4 104 41-172 32-135 (140)
35 TIGR02696 pppGpp_PNP guanosine 97.0 0.0013 2.8E-08 66.3 5.8 61 145-205 587-651 (719)
36 TIGR03591 polynuc_phos polyrib 96.9 0.0012 2.7E-08 66.2 5.3 61 145-205 560-622 (684)
37 KOG2190 PolyC-binding proteins 96.8 0.004 8.6E-08 60.4 7.7 148 41-193 138-320 (485)
38 KOG1588 RNA-binding protein Sa 96.8 0.0016 3.5E-08 58.3 4.2 29 146-174 108-136 (259)
39 TIGR03591 polynuc_phos polyrib 96.6 0.0035 7.5E-08 63.0 6.1 63 42-109 552-614 (684)
40 KOG0119 Splicing factor 1/bran 96.5 0.0044 9.4E-08 60.0 5.7 66 146-211 154-244 (554)
41 PRK04163 exosome complex RNA-b 96.2 0.018 3.9E-07 50.6 7.2 59 144-202 153-213 (235)
42 COG1185 Pnp Polyribonucleotide 96.0 0.012 2.6E-07 58.9 5.7 69 42-115 553-621 (692)
43 KOG2192 PolyC-binding hnRNP-K 95.9 0.044 9.6E-07 49.9 8.5 136 43-199 50-194 (390)
44 PLN00207 polyribonucleotide nu 95.9 0.0078 1.7E-07 62.1 4.1 61 145-205 694-757 (891)
45 TIGR01952 nusA_arch NusA famil 95.7 0.023 5.1E-07 46.6 5.6 100 43-172 35-136 (141)
46 COG1185 Pnp Polyribonucleotide 95.5 0.02 4.3E-07 57.4 5.0 61 145-205 561-623 (692)
47 PF13014 KH_3: KH domain 95.3 0.02 4.3E-07 37.0 3.1 27 52-78 2-28 (43)
48 PRK02821 hypothetical protein; 95.2 0.014 3.1E-07 43.3 2.3 31 145-178 40-70 (77)
49 COG0195 NusA Transcription elo 95.1 0.041 9E-07 47.3 5.1 101 45-175 80-181 (190)
50 cd02134 NusA_KH NusA_K homolog 95.0 0.02 4.3E-07 40.1 2.6 27 145-171 34-60 (61)
51 PRK11824 polynucleotide phosph 94.8 0.03 6.4E-07 56.5 3.9 60 146-205 564-625 (693)
52 PLN00207 polyribonucleotide nu 94.7 0.036 7.7E-07 57.4 4.3 63 42-109 686-749 (891)
53 PRK00468 hypothetical protein; 94.5 0.02 4.4E-07 42.2 1.6 22 146-167 40-61 (75)
54 PRK04163 exosome complex RNA-b 94.5 0.094 2E-06 46.1 6.1 62 42-108 146-207 (235)
55 PF13083 KH_4: KH domain; PDB: 94.4 0.0033 7.3E-08 45.2 -2.8 29 147-175 40-68 (73)
56 COG5176 MSL5 Splicing factor ( 94.2 0.12 2.5E-06 45.6 5.9 61 145-205 163-228 (269)
57 PRK01064 hypothetical protein; 94.2 0.024 5.3E-07 42.1 1.4 32 146-177 40-71 (78)
58 KOG2191 RNA-binding protein NO 94.1 0.11 2.3E-06 48.6 5.8 157 42-215 133-332 (402)
59 PF14611 SLS: Mitochondrial in 93.7 2.5 5.4E-05 35.9 13.0 137 41-202 26-169 (210)
60 COG1094 Predicted RNA-binding 93.2 0.31 6.6E-06 42.2 6.6 66 144-209 16-88 (194)
61 KOG2279 Kinase anchor protein 93.0 0.061 1.3E-06 52.8 2.3 130 40-193 67-204 (608)
62 COG1837 Predicted RNA-binding 92.6 0.078 1.7E-06 39.4 1.8 19 147-165 41-59 (76)
63 PRK11824 polynucleotide phosph 92.1 0.14 3.1E-06 51.7 3.6 62 43-109 556-617 (693)
64 cd02409 KH-II KH-II (K homolo 91.6 0.15 3.3E-06 34.6 2.3 23 147-169 36-58 (68)
65 cd02414 jag_KH jag_K homology 91.5 0.11 2.3E-06 37.9 1.5 26 147-172 35-60 (77)
66 KOG2814 Transcription coactiva 91.1 0.36 7.8E-06 44.9 4.8 65 141-205 62-135 (345)
67 COG1097 RRP4 RNA-binding prote 90.4 1.1 2.3E-05 40.0 7.0 51 147-197 157-209 (239)
68 KOG0336 ATP-dependent RNA heli 89.4 0.52 1.1E-05 45.7 4.5 52 146-197 57-112 (629)
69 KOG2192 PolyC-binding hnRNP-K 87.3 1.7 3.6E-05 39.9 6.1 64 39-107 313-381 (390)
70 COG1702 PhoH Phosphate starvat 86.0 1.7 3.7E-05 40.7 5.7 47 147-193 26-72 (348)
71 cd02134 NusA_KH NusA_K homolog 84.4 0.9 1.9E-05 31.7 2.4 37 40-76 24-60 (61)
72 COG5176 MSL5 Splicing factor ( 83.3 2.8 6E-05 37.2 5.4 78 25-107 134-218 (269)
73 COG1159 Era GTPase [General fu 81.8 3.1 6.7E-05 38.3 5.4 57 114-171 198-273 (298)
74 COG1847 Jag Predicted RNA-bind 80.7 1.1 2.4E-05 39.2 2.0 50 147-196 102-161 (208)
75 KOG0119 Splicing factor 1/bran 79.7 4.8 0.0001 39.6 6.2 85 22-109 121-229 (554)
76 PRK12704 phosphodiesterase; Pr 79.1 5.9 0.00013 38.9 6.7 65 39-107 208-273 (520)
77 TIGR01953 NusA transcription t 77.6 3.8 8.3E-05 38.2 4.8 94 50-173 243-338 (341)
78 TIGR03319 YmdA_YtgF conserved 77.0 7 0.00015 38.4 6.6 62 39-104 202-264 (514)
79 PRK15494 era GTPase Era; Provi 76.5 5.4 0.00012 36.6 5.4 58 114-172 242-318 (339)
80 PRK00106 hypothetical protein; 76.4 7.6 0.00017 38.4 6.7 62 39-104 223-285 (535)
81 PRK12328 nusA transcription el 76.0 5.2 0.00011 37.9 5.2 94 50-172 251-344 (374)
82 PRK09202 nusA transcription el 74.1 5.3 0.00011 38.9 4.8 94 51-173 246-339 (470)
83 KOG1067 Predicted RNA-binding 73.7 2.3 5E-05 42.5 2.3 52 146-197 607-659 (760)
84 TIGR00436 era GTP-binding prot 73.6 7.6 0.00016 34.1 5.4 27 145-171 231-265 (270)
85 PRK12327 nusA transcription el 73.4 7.1 0.00015 36.8 5.4 94 50-173 245-340 (362)
86 PF07650 KH_2: KH domain syndr 72.4 0.46 9.9E-06 34.2 -2.2 33 145-177 34-67 (78)
87 KOG1067 Predicted RNA-binding 70.9 6.2 0.00013 39.7 4.5 61 43-109 599-659 (760)
88 PRK12329 nusA transcription el 69.5 8.8 0.00019 37.3 5.1 94 50-173 277-372 (449)
89 KOG2113 Predicted RNA binding 65.4 4.8 0.0001 37.6 2.4 154 41-203 26-191 (394)
90 PRK08406 transcription elongat 63.9 5.7 0.00012 32.4 2.3 26 146-171 42-67 (140)
91 cd02410 archeal_CPSF_KH The ar 58.4 65 0.0014 26.8 7.6 28 146-173 86-113 (145)
92 KOG2814 Transcription coactiva 54.9 17 0.00036 34.1 4.0 76 25-104 41-119 (345)
93 KOG2208 Vigilin [Lipid transpo 53.5 53 0.0011 33.9 7.7 124 40-188 346-478 (753)
94 PF13184 KH_5: NusA-like KH do 51.9 12 0.00026 26.9 2.1 35 145-185 17-51 (69)
95 TIGR01952 nusA_arch NusA famil 50.3 14 0.0003 30.3 2.5 26 146-171 43-68 (141)
96 smart00874 B5 tRNA synthetase 50.3 19 0.00041 25.0 2.9 67 43-112 2-70 (71)
97 COG1855 ATPase (PilT family) [ 49.8 12 0.00025 37.1 2.2 39 41-79 486-524 (604)
98 TIGR00112 proC pyrroline-5-car 49.8 14 0.00031 32.1 2.6 98 61-165 125-224 (245)
99 PRK06418 transcription elongat 47.8 16 0.00034 30.9 2.5 25 148-172 72-96 (166)
100 PRK12705 hypothetical protein; 47.3 25 0.00055 34.6 4.1 59 39-101 196-255 (508)
101 PRK00089 era GTPase Era; Revie 46.0 16 0.00034 32.2 2.3 28 145-172 236-271 (292)
102 cd02412 30S_S3_KH K homology R 43.9 14 0.0003 28.6 1.5 23 146-168 71-93 (109)
103 COG1855 ATPase (PilT family) [ 43.3 16 0.00036 36.1 2.1 30 143-172 493-522 (604)
104 PF14748 P5CR_dimer: Pyrroline 43.2 8 0.00017 29.8 0.0 62 99-165 23-85 (107)
105 PF14611 SLS: Mitochondrial in 43.1 52 0.0011 27.7 5.0 56 145-200 35-92 (210)
106 COG1097 RRP4 RNA-binding prote 42.2 65 0.0014 28.9 5.6 46 43-89 148-193 (239)
107 KOG1588 RNA-binding protein Sa 42.2 31 0.00066 31.3 3.5 38 40-77 91-134 (259)
108 KOG2208 Vigilin [Lipid transpo 39.8 42 0.0009 34.7 4.5 53 145-197 356-413 (753)
109 cd02413 40S_S3_KH K homology R 38.8 17 0.00037 26.8 1.2 28 145-172 39-66 (81)
110 cd01104 HTH_MlrA-CarA Helix-Tu 37.5 64 0.0014 21.8 3.9 30 91-120 38-67 (68)
111 KOG4369 RTK signaling protein 37.3 17 0.00038 39.6 1.4 58 139-196 1343-1408(2131)
112 PRK13764 ATPase; Provisional 37.2 23 0.0005 35.6 2.2 31 142-172 487-517 (602)
113 PF00403 HMA: Heavy-metal-asso 36.8 1.2E+02 0.0027 19.9 5.4 30 61-90 15-45 (62)
114 COG0092 RpsC Ribosomal protein 36.5 31 0.00067 30.8 2.7 69 43-119 53-126 (233)
115 PRK12548 shikimate 5-dehydroge 36.3 90 0.002 27.9 5.7 117 61-200 26-151 (289)
116 PRK07680 late competence prote 35.8 30 0.00064 30.3 2.5 96 61-164 142-241 (273)
117 KOG2279 Kinase anchor protein 35.6 25 0.00055 35.1 2.1 57 145-201 77-139 (608)
118 PRK06418 transcription elongat 35.0 34 0.00073 28.9 2.5 31 45-76 65-95 (166)
119 PRK04056 Maf-like protein; Rev 34.5 59 0.0013 27.5 4.0 37 168-206 62-103 (180)
120 TIGR02663 nifX nitrogen fixati 33.2 1.4E+02 0.003 23.1 5.6 48 155-202 52-113 (119)
121 PF08383 Maf_N: Maf N-terminal 32.7 30 0.00065 22.1 1.4 14 108-121 20-33 (35)
122 cd02411 archeal_30S_S3_KH K ho 31.9 33 0.0007 25.2 1.8 21 145-165 47-67 (85)
123 PRK06928 pyrroline-5-carboxyla 31.2 1.5E+02 0.0033 26.1 6.2 98 60-164 144-244 (277)
124 KOG2113 Predicted RNA binding 31.0 34 0.00073 32.2 2.0 54 141-194 31-88 (394)
125 PRK06476 pyrroline-5-carboxyla 30.6 88 0.0019 27.0 4.6 101 61-166 134-235 (258)
126 PRK13764 ATPase; Provisional 30.6 47 0.001 33.5 3.1 41 39-79 479-519 (602)
127 PRK02821 hypothetical protein; 29.7 77 0.0017 23.4 3.4 34 39-72 29-62 (77)
128 cd04764 HTH_MlrA-like_sg1 Heli 29.7 1E+02 0.0022 21.0 3.9 30 92-121 38-67 (67)
129 PRK07634 pyrroline-5-carboxyla 29.0 21 0.00046 30.3 0.4 96 61-164 147-244 (245)
130 PRK00258 aroE shikimate 5-dehy 28.6 80 0.0017 27.9 4.0 102 94-207 44-155 (278)
131 PTZ00084 40S ribosomal protein 28.4 1.7E+02 0.0037 25.8 5.9 74 43-119 46-121 (220)
132 TIGR03675 arCOG00543 arCOG0054 27.6 1.5E+02 0.0031 30.0 6.0 91 76-173 21-130 (630)
133 COG0169 AroE Shikimate 5-dehyd 27.5 1.1E+02 0.0023 27.9 4.6 113 94-218 45-169 (283)
134 cd02414 jag_KH jag_K homology 26.2 56 0.0012 23.4 2.1 38 40-77 23-60 (77)
135 KOG0336 ATP-dependent RNA heli 26.2 59 0.0013 32.0 2.8 48 39-86 45-92 (629)
136 PF13184 KH_5: NusA-like KH do 25.7 73 0.0016 22.8 2.7 33 44-76 6-44 (69)
137 PF03958 Secretin_N: Bacterial 25.2 1E+02 0.0022 21.5 3.4 32 164-195 43-76 (82)
138 COG0345 ProC Pyrroline-5-carbo 25.0 96 0.0021 28.0 3.9 62 99-165 179-241 (266)
139 PF03484 B5: tRNA synthetase B 24.9 37 0.0008 24.0 1.0 65 43-111 2-68 (70)
140 cd00336 Ribosomal_L22 Ribosoma 24.9 73 0.0016 24.2 2.7 27 94-121 9-35 (105)
141 TIGR00507 aroE shikimate 5-deh 24.7 1E+02 0.0022 27.1 3.9 100 94-206 39-147 (270)
142 TIGR01044 rplV_bact ribosomal 24.0 78 0.0017 24.3 2.7 26 95-121 8-33 (103)
143 cd04763 HTH_MlrA-like Helix-Tu 24.0 1.5E+02 0.0032 20.2 3.9 31 91-121 38-68 (68)
144 PF11181 YflT: Heat induced st 23.6 63 0.0014 24.4 2.1 29 177-205 1-30 (103)
145 TIGR01008 rpsC_E_A ribosomal p 23.3 2.2E+02 0.0047 24.6 5.6 68 43-118 40-112 (195)
146 PRK11901 hypothetical protein; 22.9 84 0.0018 29.4 3.1 22 175-196 284-305 (327)
147 KOG3273 Predicted RNA-binding 22.0 1.4E+02 0.0031 26.5 4.2 65 50-121 178-242 (252)
148 TIGR02517 type_II_gspD general 22.0 4.2E+02 0.009 26.1 8.0 118 59-195 8-154 (594)
149 CHL00034 rpl22 ribosomal prote 21.9 84 0.0018 24.8 2.6 27 94-121 18-44 (117)
150 PF03958 Secretin_N: Bacterial 21.6 2.6E+02 0.0056 19.4 4.9 34 69-107 43-76 (82)
151 PRK14361 Maf-like protein; Pro 21.0 1.3E+02 0.0028 25.6 3.7 26 178-205 74-99 (187)
152 PRK00468 hypothetical protein; 20.7 1E+02 0.0022 22.6 2.6 31 39-69 28-58 (75)
153 TIGR02985 Sig70_bacteroi1 RNA 20.4 83 0.0018 24.1 2.2 23 197-219 139-161 (161)
154 PLN02688 pyrroline-5-carboxyla 20.0 47 0.001 28.6 0.9 55 106-165 187-241 (266)
No 1
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=100.00 E-value=3e-60 Score=402.07 Aligned_cols=179 Identities=36% Similarity=0.551 Sum_probs=175.2
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHH
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIA 118 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~ 118 (219)
..+++.++||++|+++|+|.||+++++|+++++++++||+++++|+|+|+..|.||++++||+|+|+||+|||+||+|++
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~ 85 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALK 85 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHH
Confidence 46678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCchHHHHHHHHHHHHcC
Q 027782 119 LLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFANIKIARDSLCSLILG 198 (219)
Q Consensus 119 Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~i~~Ar~aI~~Li~g 198 (219)
||+ ||++|++|+|.|++.++++||+|++|||||++|+|+++||++|||+|+|+|+||||||.|+++++||+||+|||+|
T Consensus 86 LL~-d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 86 LLE-DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGKTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred Hhc-CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCcEEEEecChhhhHHHHHHHHHHHcC
Confidence 999 8999999999999988889999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChhhhHHHHHHHHHHhhc
Q 027782 199 SPAGKVYSKLRAVTARLAER 218 (219)
Q Consensus 199 ~~~~~VY~~l~~~~~~~~~~ 218 (219)
++|++||+||++.++++|+|
T Consensus 165 ~~h~~Vy~fLer~~~~lk~~ 184 (194)
T COG1094 165 APHGKVYKFLERKERELKER 184 (194)
T ss_pred CCchhHHHHHHHHHHHHHHH
Confidence 99999999999999999987
No 2
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-58 Score=394.09 Aligned_cols=197 Identities=70% Similarity=1.124 Sum_probs=194.0
Q ss_pred CCCCCCcCCCCCCCCCceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHH
Q 027782 23 LKPLFEPLKAHEMSDGRVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCAD 102 (219)
Q Consensus 23 ~~~~~~p~~~~~~~~~~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d 102 (219)
.+|.|.|.++........++|+|+||++|+.+|+..|.+||.||+|+++++|+||.+.++|++++|..|.||.+++|+.|
T Consensus 56 ~~~~~~p~~a~~~~~~k~e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK~r~VelRt~~~t~D~s~Lqk~ad 135 (252)
T KOG3273|consen 56 PKPTFAPLKAKRKRGGKIETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLKARSVELRTCKDTEDPSALQKGAD 135 (252)
T ss_pred CCCCCCCccccccccCccceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecccceeEeecCCCCCChHHHHHHHH
Confidence 67889999999988788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCChHHHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCC
Q 027782 103 FVHAFMLGFDVIDAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSF 182 (219)
Q Consensus 103 ~I~Ai~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~ 182 (219)
||+||..||+++||++||++||+|+|+|+|.|||.|.++|++|++|||+|++|+|+.+||+.|.++|+++|.+|||+|.|
T Consensus 136 fv~Af~lGF~i~DAiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad~kIHiLG~~ 215 (252)
T KOG3273|consen 136 FVRAFILGFDIDDAIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLADSKIHILGAF 215 (252)
T ss_pred HHHHHHhCCcchhHHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecCceEEEeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHcCCCChhhhHHHHHHHHHHhhcC
Q 027782 183 ANIKIARDSLCSLILGSPAGKVYSKLRAVTARLAERF 219 (219)
Q Consensus 183 ~~i~~Ar~aI~~Li~g~~~~~VY~~l~~~~~~~~~~~ 219 (219)
+|+++||+|||.||.|++||+||+.|+.+++|++|||
T Consensus 216 ~niriAR~avcsLIlGsppgkVy~~LR~vasRl~Er~ 252 (252)
T KOG3273|consen 216 QNIRIARDAVCSLILGSPPGKVYGNLRNVASRLKERY 252 (252)
T ss_pred hhhHHHHHhhHhhhccCCchhHHHHHHHHHHhhhhcC
Confidence 9999999999999999999999999999999999997
No 3
>PRK13763 putative RNA-processing protein; Provisional
Probab=100.00 E-value=1.8e-45 Score=310.13 Aligned_cols=175 Identities=27% Similarity=0.391 Sum_probs=169.7
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhh
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALL 120 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll 120 (219)
.+..++||++++++|||.||++++.|++++|++|+||.++++|.|.|+. ++||.++++|+++|+|+++||+||+|++++
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e~A~~l~ 81 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPEKALRLL 81 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHHHHHHHh
Confidence 4578999999999999999999999999999999999998999999998 999999999999999999999999999999
Q ss_pred hcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCchHHHHHHHHHHHHcCCC
Q 027782 121 RLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFANIKIARDSLCSLILGSP 200 (219)
Q Consensus 121 ~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~i~~Ar~aI~~Li~g~~ 200 (219)
. |++++++++|.++ ..+++|++|++|||||++|+|+++||++|||+|.|++++|+|+|++++++.|+++|++|++|++
T Consensus 82 g-d~y~~~Vi~i~~~-~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 82 D-DDYVLEVIDLSDY-GDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDPEQVEIAREAIEMLIEGAP 159 (180)
T ss_pred C-CCceEEEEEhhhc-cCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCCEEEEEeCHHHHHHHHHHHHHHHcCCC
Confidence 9 9999999999999 4688999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhhHHHHHHHHHHhhc
Q 027782 201 AGKVYSKLRAVTARLAER 218 (219)
Q Consensus 201 ~~~VY~~l~~~~~~~~~~ 218 (219)
|++||++|+..++++|.|
T Consensus 160 ~~~~~~~l~~~~~~~~~~ 177 (180)
T PRK13763 160 HGTVYKFLERKKRELKRR 177 (180)
T ss_pred cHHHHHHHHHHHHHHHHh
Confidence 999999999999999876
No 4
>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=100.00 E-value=1.8e-45 Score=307.90 Aligned_cols=170 Identities=28% Similarity=0.418 Sum_probs=164.3
Q ss_pred EeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhhcCc
Q 027782 45 VNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALLRLDE 124 (219)
Q Consensus 45 I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~~Dd 124 (219)
+.||+++++.|||+||++++.|++.+|++|+||.+++.|.|+ ..++||+++++|+++|+|+++||+||+|++|+. |+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~--~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~l~g-d~ 78 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIE--EEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD-DD 78 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEe--cCCCCHHHHHHHHHHHHHHHcCCCHHHHHHhcC-Cc
Confidence 689999999999999999999999999999999998999997 567999999999999999999999999999999 99
Q ss_pred ceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCchHHHHHHHHHHHHcCCCChhh
Q 027782 125 LYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFANIKIARDSLCSLILGSPAGKV 204 (219)
Q Consensus 125 ~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~i~~Ar~aI~~Li~g~~~~~V 204 (219)
+++++++|.++ ..+++|+.|++|||||++|+|+++||++|||+|+|++++|+|+|+++++++||++|++|++|++|++|
T Consensus 79 y~~~Vi~I~~~-~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~~~v~i~G~~~~~~~A~~~i~~li~~~~~~~v 157 (172)
T TIGR03665 79 YMLEVIDLKEY-GKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIGDPEQVQIAREAIEMLIEGAPHGTV 157 (172)
T ss_pred ceEEEEEhhhc-cCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcCCEEEEECCHHHHHHHHHHHHHHHcCCCChhH
Confidence 99999999999 46889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHhhc
Q 027782 205 YSKLRAVTARLAER 218 (219)
Q Consensus 205 Y~~l~~~~~~~~~~ 218 (219)
|+|||+.++.+|-|
T Consensus 158 y~~l~~~~~~~~~~ 171 (172)
T TIGR03665 158 YKFLERKRRELKRR 171 (172)
T ss_pred HHHHHHHHHHHhhc
Confidence 99999999998764
No 5
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=4.4e-38 Score=278.73 Aligned_cols=183 Identities=19% Similarity=0.217 Sum_probs=170.4
Q ss_pred CCCCCCcCCCCCCCCCceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHH
Q 027782 23 LKPLFEPLKAHEMSDGRVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCAD 102 (219)
Q Consensus 23 ~~~~~~p~~~~~~~~~~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d 102 (219)
..+.|.+.++|++ ..+.+++..+||+||..||+..|..+.+.|.++ ++.+.+|+.+|++.|.|+..|+|||.++||+|
T Consensus 40 ki~~Fs~edn~~g-~~EeSSfatlFPKYREkYlke~wp~v~raL~e~-~i~c~lDL~egsm~V~TtRkT~DPyIiikArd 117 (356)
T KOG2874|consen 40 KIEKFSKEDNPHG-FLEESSFATLFPKYREKYLKECWPLVERALDEH-HIKCVLDLVEGSMTVKTTRKTRDPYIIIKARD 117 (356)
T ss_pred cccccCcccCccc-hhhhhhHHhhhHHHHHHHHHHHHHHHHHHHHhc-CcceEEeeccceeEEeecccccCceeeeeHHH
Confidence 5688999999885 458999999999999999999999999998766 99999999999999999999999999999999
Q ss_pred HHHHHHcCCChHHHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCC
Q 027782 103 FVHAFMLGFDVIDAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSF 182 (219)
Q Consensus 103 ~I~Ai~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~ 182 (219)
||++++||+++++|+++|+ ||++||+|+|..+.. +.+.|.+++.|+||++|.|+++||.+|+|||.|+|+||++||+|
T Consensus 118 lIKLlaRsVp~eqAvkiLq-Dev~CdiIkIgn~V~-nkerFvKRRqRLiGpng~TLKAlelLT~CYilVqG~TVsaiGpf 195 (356)
T KOG2874|consen 118 LIKLLARSVPFEQAVKILQ-DEVACDIIKIGNLVR-NKERFVKRRQRLIGPNGSTLKALELLTNCYILVQGNTVSAIGPF 195 (356)
T ss_pred HHHHHHcCCCHHHHHHHHh-hccceeeeehhhhhc-cHHHHHHHHHHhcCCCchhHHHHHHHhhcEEEeeCcEEEeecCc
Confidence 9999999999999999999 999999999999885 78999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHcCCCChhhhHHHHHH
Q 027782 183 ANIKIARDSLCSLILGSPAGKVYSKLRAV 211 (219)
Q Consensus 183 ~~i~~Ar~aI~~Li~g~~~~~VY~~l~~~ 211 (219)
.+++.+|+.+++||.+-+| +|+-=+-+
T Consensus 196 kGlkevr~IV~DcM~NiHP--iY~IK~Lm 222 (356)
T KOG2874|consen 196 KGLKEVRKIVEDCMKNIHP--IYNIKTLM 222 (356)
T ss_pred chHHHHHHHHHHHHhccch--HHHHHHHH
Confidence 9999999999999988443 67654433
No 6
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.55 E-value=3.1e-14 Score=137.08 Aligned_cols=151 Identities=15% Similarity=0.169 Sum_probs=115.7
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceE--EEEeCCCCCCHHHHHHHHHHHHHHHcC-CChHH
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRV--ELKTRADTPDISNLQKCADFVHAFMLG-FDVID 115 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V--~I~~~~~t~dp~~i~KA~d~I~Ai~rG-F~~e~ 115 (219)
...+.+|.||.+|+++|||+.|++++.|++.++|++.+.-+.... ..++...|+||+.+..|+.+|..|.+- +.=-.
T Consensus 137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~ve~a~~lV~dil~e~~~~~~ 216 (600)
T KOG1676|consen 137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKVEQAKQLVADILREEDDEVP 216 (600)
T ss_pred cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHHHHHHHHHHHHHHhcccCCC
Confidence 467899999999999999999999999999999999887543322 245666789999999999999999761 11000
Q ss_pred HH-HhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc--------CceEEEeeCCchHH
Q 027782 116 AI-ALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA--------DTKIHILGSFANIK 186 (219)
Q Consensus 116 A~-~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~--------~~tV~IiG~~~~i~ 186 (219)
.. --...+..--..++| +.++-.+|-||||+|+++|.|++-||++|.+. ++++.|||+.+.|+
T Consensus 217 g~~~~~g~~~g~~~~~~V--------~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie 288 (600)
T KOG1676|consen 217 GSGGHAGVRGGGSATREV--------KVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIE 288 (600)
T ss_pred ccccccCcCccccceeEE--------eccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHH
Confidence 00 001101111113443 24555799999999999999999999999995 24699999999999
Q ss_pred HHHHHHHHHHc
Q 027782 187 IARDSLCSLIL 197 (219)
Q Consensus 187 ~Ar~aI~~Li~ 197 (219)
.|.+.|..||.
T Consensus 289 ~Aa~lI~eii~ 299 (600)
T KOG1676|consen 289 HAAELINEIIA 299 (600)
T ss_pred HHHHHHHHHHH
Confidence 99999999995
No 7
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=99.23 E-value=2.3e-11 Score=117.31 Aligned_cols=63 Identities=33% Similarity=0.474 Sum_probs=56.8
Q ss_pred ccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCce-EEEeeCCchH--HHHHHHHHHHH-cCCCChh
Q 027782 138 LRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTK-IHILGSFANI--KIARDSLCSLI-LGSPAGK 203 (219)
Q Consensus 138 ~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V~IiG~~~~i--~~Ar~aI~~Li-~g~~~~~ 203 (219)
+..+.+ +|||||++|+|+|++|.+|||+|+|+|+. +.++++|+++ ++||.+++.|| +|++|..
T Consensus 210 lp~d~~---kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp~ 276 (514)
T TIGR03319 210 LPNDEM---KGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHPA 276 (514)
T ss_pred cCChhh---hccccCCCcchHHHHHHHhCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCHH
Confidence 345565 99999999999999999999999999987 8889999999 59999999999 6997763
No 8
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.22 E-value=5.6e-11 Score=111.46 Aligned_cols=142 Identities=18% Similarity=0.179 Sum_probs=108.6
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCC-ceEEEEeCCCCCCHHHHHHHHHHHHHHH---cCCChH
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKA-RRVELKTRADTPDISNLQKCADFVHAFM---LGFDVI 114 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~-~~V~I~~~~~t~dp~~i~KA~d~I~Ai~---rGF~~e 114 (219)
+.++..+.||..-+|+|||+.|..+|.|....|.+|.|.+-+ -.|..|-...|++|.+.+||+--|..-. -.|.|.
T Consensus 409 e~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikEenf~~Pk 488 (584)
T KOG2193|consen 409 EQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLPK 488 (584)
T ss_pred chhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCch
Confidence 567888999999999999999999999999999999996422 1122222223589999999997775432 123343
Q ss_pred HHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC--------ce-EEEeeCCchH
Q 027782 115 DAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD--------TK-IHILGSFANI 185 (219)
Q Consensus 115 ~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~--------~t-V~IiG~~~~i 185 (219)
+-++|-- +| ..++++.||+|||||+|.+.|+++|++.++|.. .+ |-|||.|-.-
T Consensus 489 eevklet---------hi--------rVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyat 551 (584)
T KOG2193|consen 489 EEVKLET---------HI--------RVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYAT 551 (584)
T ss_pred hhheeee---------ee--------eccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcc
Confidence 3222211 11 357899999999999999999999999999962 13 7889999999
Q ss_pred HHHHHHHHHHHc
Q 027782 186 KIARDSLCSLIL 197 (219)
Q Consensus 186 ~~Ar~aI~~Li~ 197 (219)
..|..-|..|+.
T Consensus 552 q~aQrki~~iv~ 563 (584)
T KOG2193|consen 552 QNAQRKIAHIVN 563 (584)
T ss_pred hHHHHHHHHHHH
Confidence 999998888874
No 9
>PRK00106 hypothetical protein; Provisional
Probab=99.17 E-value=7e-11 Score=114.43 Aligned_cols=62 Identities=34% Similarity=0.520 Sum_probs=56.0
Q ss_pred ccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCce-EEEeeCCchHH--HHHHHHHHHH-cCCCCh
Q 027782 138 LRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTK-IHILGSFANIK--IARDSLCSLI-LGSPAG 202 (219)
Q Consensus 138 ~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V~IiG~~~~i~--~Ar~aI~~Li-~g~~~~ 202 (219)
+..+.+ +|||||++|+|+|++|.+|||+|+|+|+. +.++++|++++ +||.++++|| +|++|.
T Consensus 231 lp~dem---kGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~fdpvRReiAr~~le~Li~dgrIhp 296 (535)
T PRK00106 231 LPDDNM---KGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSGFDPIRREIARMTLESLIKDGRIHP 296 (535)
T ss_pred cCChHh---hcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeCCChHHHHHHHHHHHHHHHcCCcCH
Confidence 345566 99999999999999999999999999987 88899999995 9999999999 599775
No 10
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.17 E-value=5.1e-11 Score=115.11 Aligned_cols=145 Identities=14% Similarity=0.219 Sum_probs=114.1
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCC------ceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKA------RRVELKTRADTPDISNLQKCADFVHAFMLGFD 112 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~------~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~ 112 (219)
...++.|.||...+|.|||+.|+++|.|...+|++|.|-.++ +++.|. +.+.-+..|..+|.+|..+.+
T Consensus 228 ~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~Ii-----G~~d~ie~Aa~lI~eii~~~~ 302 (600)
T KOG1676|consen 228 GSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQII-----GTVDQIEHAAELINEIIAEAE 302 (600)
T ss_pred ccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeee-----cCHHHHHHHHHHHHHHHHHHh
Confidence 455899999999999999999999999999999999996544 455555 688999999999999964332
Q ss_pred hHH-------HHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc---------CceE
Q 027782 113 VID-------AIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA---------DTKI 176 (219)
Q Consensus 113 ~e~-------A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~---------~~tV 176 (219)
-.. +-.++. .|.+. .+.-.+|.+|||+|+|+|.|+..||+++-+. .+++
T Consensus 303 ~~~~~~~~~G~P~~~~-------~fy~~--------VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf 367 (600)
T KOG1676|consen 303 AGAGGGMGGGAPGLVA-------QFYMK--------VPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTF 367 (600)
T ss_pred ccCCCCcCCCCcccee-------eEEEe--------ccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEE
Confidence 211 111111 13321 2344599999999999999999999999885 3478
Q ss_pred EEeeCCchHHHHHHHHHHHHcCCCChh
Q 027782 177 HILGSFANIKIARDSLCSLILGSPAGK 203 (219)
Q Consensus 177 ~IiG~~~~i~~Ar~aI~~Li~g~~~~~ 203 (219)
.|-|+..+|..|+..|...+.+-.+.+
T Consensus 368 ~IrG~~~QIdhAk~LIr~kvg~~~~n~ 394 (600)
T KOG1676|consen 368 VIRGDKRQIDHAKQLIRDKVGDIAPNT 394 (600)
T ss_pred EEecCcccchHHHHHHHHHhcccCCCC
Confidence 999999999999999999997654444
No 11
>PRK12704 phosphodiesterase; Provisional
Probab=99.05 E-value=3.8e-10 Score=109.08 Aligned_cols=62 Identities=34% Similarity=0.486 Sum_probs=55.9
Q ss_pred ccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCce-EEEeeCCchHH--HHHHHHHHHH-cCCCCh
Q 027782 138 LRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTK-IHILGSFANIK--IARDSLCSLI-LGSPAG 202 (219)
Q Consensus 138 ~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V~IiG~~~~i~--~Ar~aI~~Li-~g~~~~ 202 (219)
+..+.+ +|||||++|+|+|++|.+|||+|+|+|+. +.++.+|++++ +|+.+++.|+ .|.+|.
T Consensus 216 lp~d~m---kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P 281 (520)
T PRK12704 216 LPNDEM---KGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHP 281 (520)
T ss_pred cCCchh---hcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCC
Confidence 344555 99999999999999999999999999986 88899999998 9999999999 588664
No 12
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.82 E-value=1.4e-07 Score=86.52 Aligned_cols=153 Identities=18% Similarity=0.161 Sum_probs=104.8
Q ss_pred eeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC-------CceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Q 027782 40 VQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK-------ARRVELKTRADTPDISNLQKCADFVHAFMLGFD 112 (219)
Q Consensus 40 ~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~-------~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~ 112 (219)
.-..+|.||.+-.|.|||+.|+++..|+..+|+.|++--. +..|-+ .++...+++-..+||..-.|.-.
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcl----i~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCL----IQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEE----EeccHHHHHHHHHHHHHHHHHhH
Confidence 3678999999999999999999999999999999999632 233332 34678899999999988766433
Q ss_pred hHHHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC----------ceEEEeeCC
Q 027782 113 VIDAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD----------TKIHILGSF 182 (219)
Q Consensus 113 ~e~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~----------~tV~IiG~~ 182 (219)
-..+- ..+.++..- .=-+..++-.. +.--.|.||||+|-|+|.|.+.+||.|.|+. .-|.+.|.+
T Consensus 114 ~~~~k-~v~~~~pqt-~~r~kqikivv---PNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~ 188 (402)
T KOG2191|consen 114 QAVAK-PVDILQPQT-PDRIKQIKIVV---PNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP 188 (402)
T ss_pred HhhcC-CccccCCCC-ccccceeEEec---cCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH
Confidence 22221 000000000 00001111111 2234799999999999999999999999982 236778999
Q ss_pred chHHHHHHHHHHHHcCCCC
Q 027782 183 ANIKIARDSLCSLILGSPA 201 (219)
Q Consensus 183 ~~i~~Ar~aI~~Li~g~~~ 201 (219)
++...|-..|...|.--||
T Consensus 189 e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 189 EQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred HHHHHHHHHHHHHhhcCCc
Confidence 9998777777666654444
No 13
>PRK12705 hypothetical protein; Provisional
Probab=98.71 E-value=1.9e-08 Score=97.08 Aligned_cols=62 Identities=31% Similarity=0.454 Sum_probs=54.9
Q ss_pred ccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCce-EEEeeCCchH--HHHHHHHHHHH-cCCCCh
Q 027782 138 LRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTK-IHILGSFANI--KIARDSLCSLI-LGSPAG 202 (219)
Q Consensus 138 ~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V~IiG~~~~i--~~Ar~aI~~Li-~g~~~~ 202 (219)
+..+.+ +|||||++|+++|++|.+||++|+|+|.. +.++.+|+++ ++|+.+++.|+ .|..|.
T Consensus 204 lp~dem---kGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~fdp~rreia~~~l~~Li~dgri~p 269 (508)
T PRK12705 204 IPSDAM---KGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISSFNPIRREIARLTLEKLLADGRIHP 269 (508)
T ss_pred cCChHh---hccccCccchhHHHHHHhhCCceEecCCccchhhcccCccchHHHHHHHHHHHhcCCCCh
Confidence 344555 99999999999999999999999999976 7789999999 59999999999 588665
No 14
>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=98.61 E-value=6.1e-08 Score=68.29 Aligned_cols=50 Identities=28% Similarity=0.287 Sum_probs=44.3
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcCc-eEEEeeC-CchHHHHHHHHH
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIADT-KIHILGS-FANIKIARDSLC 193 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~-tV~IiG~-~~~i~~Ar~aI~ 193 (219)
...+|+|||++|.+++.|++.|||+|.|.++ .|.|.|+ .++++.|++.|+
T Consensus 10 ~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 10 PDKIRDVIGPGGKTIKKIIEETGVKIDIEDDGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred hhheeeeECCCchHHHHHHHHHCCEEEeCCCCEEEEEeCCHHHHHHHHHHhC
Confidence 3458999999999999999999999999874 5999998 889999998763
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=98.57 E-value=5.5e-08 Score=67.23 Aligned_cols=49 Identities=33% Similarity=0.466 Sum_probs=44.7
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcCc----eEEEeeCCchHHHHHHHH
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIADT----KIHILGSFANIKIARDSL 192 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~----tV~IiG~~~~i~~Ar~aI 192 (219)
....|+|||++|.+++.||..|||.|.|.++ .|.|.|+.++++.|++.|
T Consensus 8 ~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 8 SSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp HHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEESHHHHHHHHHHH
T ss_pred HHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEeCHHHHHHHHhhC
Confidence 4569999999999999999999999999873 699999999999999875
No 16
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=98.55 E-value=1.9e-07 Score=88.14 Aligned_cols=135 Identities=21% Similarity=0.279 Sum_probs=99.8
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEc------CCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHH
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNL------KARRVELKTRADTPDISNLQKCADFVHAFMLGFDVID 115 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~------~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~ 115 (219)
-..+.||-.-+|+|||+.|.+++.|..++.++|.+-- .++.++|-+ .|...-+|..+|..|.-. +
T Consensus 200 PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~-----tpEg~s~Ac~~ILeimqk----E 270 (584)
T KOG2193|consen 200 PLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHS-----TPEGTSKACKMILEIMQK----E 270 (584)
T ss_pred ceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEec-----CccchHHHHHHHHHHHHH----h
Confidence 3568899999999999999999999999999888853 246777775 466777888888877542 2
Q ss_pred HHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc----------CceEEEeeCCchH
Q 027782 116 AIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA----------DTKIHILGSFANI 185 (219)
Q Consensus 116 A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~----------~~tV~IiG~~~~i 185 (219)
|.. |++- +-+. ++.+.-|. .+||+|||.|++++-||.-|||+|.|. +.||.+-|+.+.+
T Consensus 271 A~~----~k~~-~e~p---Lk~lAHN~---lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac 339 (584)
T KOG2193|consen 271 AVD----DKVA-EEIP---LKILAHNN---LVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEAC 339 (584)
T ss_pred hhc----cchh-hhcc---hhhhhhcc---hhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHH
Confidence 221 2221 1111 22223334 499999999999999999999999984 5689999988888
Q ss_pred HHHHHHHHHHH
Q 027782 186 KIARDSLCSLI 196 (219)
Q Consensus 186 ~~Ar~aI~~Li 196 (219)
-.|..-|...+
T Consensus 340 ~~AE~eImkKl 350 (584)
T KOG2193|consen 340 VQAEAEIMKKL 350 (584)
T ss_pred HHHHHHHHHHH
Confidence 77766665544
No 17
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.53 E-value=1.6e-07 Score=65.31 Aligned_cols=49 Identities=24% Similarity=0.331 Sum_probs=44.5
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcC-----ceEEEeeCCchHHHHHHHH
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIAD-----TKIHILGSFANIKIARDSL 192 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~-----~tV~IiG~~~~i~~Ar~aI 192 (219)
....|+|||++|.+++.|+..|||+|.|.+ +.|.|.|+.+++..|+..|
T Consensus 8 ~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 8 KKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred HHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcCHHHHHHHHHHh
Confidence 466899999999999999999999999987 4599999999999888776
No 18
>smart00322 KH K homology RNA-binding domain.
Probab=98.48 E-value=4e-07 Score=61.95 Aligned_cols=52 Identities=29% Similarity=0.458 Sum_probs=47.7
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcC-----ceEEEeeCCchHHHHHHHHHHHH
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIAD-----TKIHILGSFANIKIARDSLCSLI 196 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~-----~tV~IiG~~~~i~~Ar~aI~~Li 196 (219)
...|++||++|.+++.|+..|||+|.+.+ ..+.+.|+.++++.|+..|.+++
T Consensus 12 ~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred hhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 55899999999999999999999999987 55899999999999999998876
No 19
>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=98.43 E-value=9.9e-07 Score=70.41 Aligned_cols=56 Identities=20% Similarity=0.255 Sum_probs=49.2
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCc------------------------eEEEeeCC---chHHHHHHHHHHHHcC
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADT------------------------KIHILGSF---ANIKIARDSLCSLILG 198 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~------------------------tV~IiG~~---~~i~~Ar~aI~~Li~g 198 (219)
.+|+|||++|+|+|.||..|||+|.|.|+ .|.|.+.- +.+..|.+.|+.|+.-
T Consensus 16 ~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~~ 95 (120)
T cd02395 16 FVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLKP 95 (120)
T ss_pred eeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhcc
Confidence 49999999999999999999999999986 47888865 8889999999999974
Q ss_pred CCC
Q 027782 199 SPA 201 (219)
Q Consensus 199 ~~~ 201 (219)
...
T Consensus 96 ~~~ 98 (120)
T cd02395 96 AIE 98 (120)
T ss_pred CCC
Confidence 443
No 20
>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=98.42 E-value=7.7e-07 Score=62.65 Aligned_cols=58 Identities=14% Similarity=0.245 Sum_probs=52.6
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
+..+.||+++++.|+|+.|++++.|++.+|++|.++. ++.|.|.+ .|+.++..|+++|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-~g~v~I~G----~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-DGTVYIAA----SDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-CCEEEEEe----CCHHHHHHHHHHh
Confidence 4568999999999999999999999999999999986 68999987 4688999999887
No 21
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.39 E-value=5.9e-07 Score=61.96 Aligned_cols=49 Identities=33% Similarity=0.515 Sum_probs=43.5
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcC-------ceEEEeeCCchHHHHHHHH
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIAD-------TKIHILGSFANIKIARDSL 192 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~-------~tV~IiG~~~~i~~Ar~aI 192 (219)
....|+|||++|.+++.|+..|||.|.|.. ..|.|.|+.+++..|+..|
T Consensus 8 ~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 8 SSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred hhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 356899999999999999999999999976 3489999999999988775
No 22
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.27 E-value=1.4e-06 Score=73.74 Aligned_cols=64 Identities=13% Similarity=0.028 Sum_probs=59.5
Q ss_pred ccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 51 RYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 51 Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
+.|.|||+.|++++.|++.+|++|.++. +.|.|. ++|..+..|++.|.++.+|+.++.++++|+
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~--~~v~i~-----G~~~~~~~A~~~I~~li~g~~~~~~~~~l~ 168 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG--KTVAII-----GDPEQVEIAREAIEMLIEGAPHGTVYKFLE 168 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC--CEEEEE-----eCHHHHHHHHHHHHHHHcCCCcHHHHHHHH
Confidence 7899999999999999999999999985 457765 599999999999999999999999999998
No 23
>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=98.21 E-value=3e-06 Score=59.88 Aligned_cols=50 Identities=26% Similarity=0.339 Sum_probs=43.6
Q ss_pred hhhhhcceecCCCchHHHHHHhhCceEEEcCc--------eEEEeeCCchHHHHHHHH
Q 027782 143 LSRAIGRLSGKGGKTKFAIENATKTRIVIADT--------KIHILGSFANIKIARDSL 192 (219)
Q Consensus 143 ~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~--------tV~IiG~~~~i~~Ar~aI 192 (219)
+...+|+|||++|.+++.|+..|||+|.+... .|.|.|+++++..|...|
T Consensus 7 p~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 7 PSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 34569999999999999999999999999742 378899999999998766
No 24
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=98.09 E-value=5.7e-05 Score=72.97 Aligned_cols=150 Identities=22% Similarity=0.189 Sum_probs=103.8
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC-----CceEEEEeC----CCCCCHHHHHHHHHHHHHHHc
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK-----ARRVELKTR----ADTPDISNLQKCADFVHAFML 109 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~-----~~~V~I~~~----~~t~dp~~i~KA~d~I~Ai~r 109 (219)
...++.+..|--.+|-+||+.|++++.|...+..+++++.. ++-|+|.++ ..-+.-.++.||.++|-+.
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~-- 118 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFK-- 118 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhc--
Confidence 45558899999999999999999999999888888888754 345555540 0012446888888876543
Q ss_pred CCChHHHHHhhhcCcceeeeEEecccc-cccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCc--------eEEEee
Q 027782 110 GFDVIDAIALLRLDELYVESFEIKDVK-TLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADT--------KIHILG 180 (219)
Q Consensus 110 GF~~e~A~~Ll~~Dd~~~e~i~I~dv~-~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~--------tV~IiG 180 (219)
|..++ .. .. |.-..+... .+. +| =..+-.+|=||||+|..++.|.+.|||+|.|-++ .|-|-|
T Consensus 119 -~~~d~-~~-~~-d~~~~~~~~--~v~~RL--lVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG 190 (485)
T KOG2190|consen 119 -LEEDD-EA-AE-DNGEDASGP--EVTCRL--LVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISG 190 (485)
T ss_pred -ccccc-cc-cc-cCCccccCC--ceEEEE--EechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcC
Confidence 22111 10 00 100000011 011 11 1234569999999999999999999999999755 388889
Q ss_pred CCchHHHHHHHHHHHHcC
Q 027782 181 SFANIKIARDSLCSLILG 198 (219)
Q Consensus 181 ~~~~i~~Ar~aI~~Li~g 198 (219)
..+.|..|-..|+.+|..
T Consensus 191 ~~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 191 EPDAVKKALVQISSRLLE 208 (485)
T ss_pred chHHHHHHHHHHHHHHHh
Confidence 999999999999999964
No 25
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.00 E-value=9.7e-06 Score=55.88 Aligned_cols=58 Identities=12% Similarity=0.143 Sum_probs=51.0
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC--CceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK--ARRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~--~~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
|.++.||...+++|+|+.|..++.|++.++++|.+... ...|.|.+ ++..+.+|+++|
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 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDDDERDIVTISG-----SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEESTTEEEEEEEEE-----SHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCCCCcEEEEEEe-----CHHHHHHHHhhC
Confidence 56899999999999999999999999999999999864 34677774 789999999876
No 26
>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=97.84 E-value=4.1e-05 Score=53.04 Aligned_cols=57 Identities=14% Similarity=0.174 Sum_probs=50.7
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC---CceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK---ARRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~---~~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
.++.||+...+.|+|+.|..++.|++.+|++|.+... ++.|.|.+ ++.++.+|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G-----~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITG-----PKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEc-----CHHHHHHHHHHh
Confidence 4689999999999999999999999999999999864 68888885 578888888776
No 27
>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=97.84 E-value=3.7e-05 Score=54.25 Aligned_cols=58 Identities=19% Similarity=0.156 Sum_probs=50.1
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCC------ceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKA------RRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~------~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
+.++.||.+.++.|+|++|..++.|.+.+|++|++.... +.|+|. +++..+.+|..+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~-----G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTIS-----GKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEE-----eCHHHHHHHHHhh
Confidence 357899999999999999999999999999999997543 456676 5789999998876
No 28
>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=97.81 E-value=3.5e-05 Score=64.70 Aligned_cols=59 Identities=29% Similarity=0.342 Sum_probs=51.0
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcCc--eEEE---eeCCchHHHHHHHHHHHHcCCCCh
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIADT--KIHI---LGSFANIKIARDSLCSLILGSPAG 202 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~--tV~I---iG~~~~i~~Ar~aI~~Li~g~~~~ 202 (219)
...+|.|||++|++++.||..|||+|.+.++ +|.| -++.+.+..|++.|..+..|-.+.
T Consensus 6 ~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e 69 (172)
T TIGR03665 6 KDRIGVLIGKGGETKKEIEERTGVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE 69 (172)
T ss_pred HHHhhhHhCCchhHHHHHHHHhCcEEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence 3468999999999999999999999999986 4666 488889999999999998875444
No 29
>PF13014 KH_3: KH domain
Probab=97.80 E-value=3.2e-05 Score=50.38 Aligned_cols=27 Identities=41% Similarity=0.639 Sum_probs=25.8
Q ss_pred hcceecCCCchHHHHHHhhCceEEEcC
Q 027782 147 IGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
.|+|||++|.+++.|+..|||+|.|..
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 689999999999999999999999986
No 30
>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=97.75 E-value=8.6e-05 Score=51.01 Aligned_cols=57 Identities=16% Similarity=0.173 Sum_probs=49.4
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC-----CceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK-----ARRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~-----~~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
.++.||.+.+++|+|..|..++.|++.+++.|.+... .+.|.|.+ ++..+..|..+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G-----~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITG-----TPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEc-----CHHHHHHHHHHh
Confidence 5789999999999999999999999999999999864 46677775 478888888776
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=97.42 E-value=0.00088 Score=45.19 Aligned_cols=62 Identities=18% Similarity=0.191 Sum_probs=53.0
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC---CceEEEEeCCCCCCHHHHHHHHHHHHHH
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK---ARRVELKTRADTPDISNLQKCADFVHAF 107 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~---~~~V~I~~~~~t~dp~~i~KA~d~I~Ai 107 (219)
.+..+.||.+..+.++|+.|..++.|++.+++++.+... ...+.|.+ ++..+..|.++|...
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g-----~~~~v~~a~~~i~~~ 67 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITG-----PPENVEKAAELILEI 67 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEc-----CHHHHHHHHHHHHHH
Confidence 456799999999999999999999999999999998764 36677774 578999999888754
No 32
>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=97.23 E-value=0.00075 Score=67.97 Aligned_cols=67 Identities=10% Similarity=0.083 Sum_probs=60.3
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCh
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDV 113 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~ 113 (219)
+..+.||+++++.|||.+|++++.|.+.+|++|.|+- +|.|.|.. .|...+.+|.++|+++..-|.|
T Consensus 579 ~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-~G~V~I~a----~d~~~~~~A~~~I~~i~~~~~~ 645 (719)
T TIGR02696 579 IITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-DGTVYIGA----ADGPSAEAARAMINAIANPTMP 645 (719)
T ss_pred eEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-CcEEEEEe----CCHHHHHHHHHHHHHhhCcCcC
Confidence 3668999999999999999999999999999999995 79999987 5889999999999999876443
No 33
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.22 E-value=0.0015 Score=52.17 Aligned_cols=67 Identities=12% Similarity=0.044 Sum_probs=53.6
Q ss_pred EEeeCC------CccccchhcCccchhHHHhhcccEEEEEcCC----------------------ceEEEEeCCCCCC--
Q 027782 44 KVNVPP------HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKA----------------------RRVELKTRADTPD-- 93 (219)
Q Consensus 44 ~I~IP~------~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~----------------------~~V~I~~~~~t~d-- 93 (219)
+|.||- +.+|.|+|..|++.+.|++.+||+|.|.-.. +.|.|.. .+
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a----~~~~ 78 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITA----ETPP 78 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEe----CCcH
Confidence 455665 4579999999999999999999999998542 6677776 45
Q ss_pred HHHHHHHHHHHHHHHcCCChH
Q 027782 94 ISNLQKCADFVHAFMLGFDVI 114 (219)
Q Consensus 94 p~~i~KA~d~I~Ai~rGF~~e 114 (219)
..++.+|..+|..+...+.++
T Consensus 79 ~e~~~~A~~~I~~ll~~~~~~ 99 (120)
T cd02395 79 EEALAKAVEAIEELLKPAIEG 99 (120)
T ss_pred HHHHHHHHHHHHHHhccCCCc
Confidence 689999999999987654443
No 34
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.08 E-value=0.0011 Score=54.31 Aligned_cols=104 Identities=14% Similarity=0.075 Sum_probs=68.4
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhh
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALL 120 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll 120 (219)
+.-.+.||+..+|..+|++|+.++.|.+.+|-+|.+ | +. +.|| +.||+.+.....+.+.. +.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdV------v--e~---s~d~------~~fI~n~l~Pa~V~~v~-I~ 93 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIEL------V--EY---SDDP------EEFIKNIFAPAAVRSVT-IK 93 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEE------E--Ec---CCCH------HHHHHHHcCCCEEEEEE-EE
Confidence 666777899999999999999999998887755544 2 21 2344 67777764444333221 11
Q ss_pred hcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 121 RLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 121 ~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
+.++- ..+.+. ....-.|+.|||+|+|++.++.++|-++-|.
T Consensus 94 ~~~~~--~~~~V~--------V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 94 KKNGD--KVAYVE--------VAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred ecCCc--EEEEEE--------ECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 10110 011110 1134489999999999999999999988663
No 35
>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=96.96 E-value=0.0013 Score=66.33 Aligned_cols=61 Identities=23% Similarity=0.297 Sum_probs=49.6
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcCc-eEEEee-CCchHHHHHHHHHHHHcC--CCChhhh
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIADT-KIHILG-SFANIKIARDSLCSLILG--SPAGKVY 205 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~-tV~IiG-~~~~i~~Ar~aI~~Li~g--~~~~~VY 205 (219)
..+|.|||++|+++|.|+..|||.|.|.++ +|.|.+ +.+.++.|++.|+.+... -.-|.+|
T Consensus 587 ~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~ 651 (719)
T TIGR02696 587 DKIGEVIGPKGKMINQIQDETGAEISIEDDGTVYIGAADGPSAEAARAMINAIANPTMPEVGERF 651 (719)
T ss_pred HHhhheeCCCcHhHHHHHHHHCCEEEEecCcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEE
Confidence 458999999999999999999999999985 577776 345678899999988863 3455555
No 36
>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=96.91 E-value=0.0012 Score=66.16 Aligned_cols=61 Identities=25% Similarity=0.331 Sum_probs=49.4
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcCc-eEEEee-CCchHHHHHHHHHHHHcCCCChhhh
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIADT-KIHILG-SFANIKIARDSLCSLILGSPAGKVY 205 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~-tV~IiG-~~~~i~~Ar~aI~~Li~g~~~~~VY 205 (219)
-.+|+|||++|++++.|++.|||.|.|.++ +|.|.+ +-..+..|++.|..+...-..|.+|
T Consensus 560 ~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~ 622 (684)
T TIGR03591 560 DKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIY 622 (684)
T ss_pred HHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEE
Confidence 358999999999999999999999999975 577765 4556689999999887654455555
No 37
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=96.81 E-value=0.004 Score=60.38 Aligned_cols=148 Identities=19% Similarity=0.212 Sum_probs=98.1
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC------CceEEEEeCCCCCCHHHHHHHHHHHHHHHcCC---
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK------ARRVELKTRADTPDISNLQKCADFVHAFMLGF--- 111 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~------~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF--- 111 (219)
-+..+.||...+|.|||+.|++++.|.+.++++|++-.+ ++.|+|. +.|.++.+|--.|-.+.+-+
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~Is-----G~~~av~~al~~Is~~L~~~~~~ 212 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTIS-----GEPDAVKKALVQISSRLLENPPR 212 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEc-----CchHHHHHHHHHHHHHHHhcCCc
Confidence 367899999999999999999999999999999999654 5667776 58899999998888877653
Q ss_pred --ChHHHHHhhhc-----CcceeeeEEec-cccc-----ccc------hhhhhhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 112 --DVIDAIALLRL-----DELYVESFEIK-DVKT-----LRG------EHLSRAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 112 --~~e~A~~Ll~~-----Dd~~~e~i~I~-dv~~-----~~~------~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
.+-.+....+- ..+.....--. ++.. ... -...-..++++|++|-.++.+++.|+.-|.|.
T Consensus 213 ~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~ 292 (485)
T KOG2190|consen 213 SPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVG 292 (485)
T ss_pred CCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEec
Confidence 22222221110 00000000000 0000 000 12234789999999999999999999999999
Q ss_pred Cce---EEEeeCCchHH----HHHHHHH
Q 027782 173 DTK---IHILGSFANIK----IARDSLC 193 (219)
Q Consensus 173 ~~t---V~IiG~~~~i~----~Ar~aI~ 193 (219)
+.. +..+...+.-+ .|.+|+.
T Consensus 293 ~~~~~~~i~~s~~e~~~~~~s~a~~a~~ 320 (485)
T KOG2190|consen 293 DSRTDRIVTISARENPEDRYSMAQEALL 320 (485)
T ss_pred cccCcceeeeccccCcccccccchhhhh
Confidence 753 24455554443 5555553
No 38
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.76 E-value=0.0016 Score=58.31 Aligned_cols=29 Identities=28% Similarity=0.466 Sum_probs=27.2
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCc
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADT 174 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~ 174 (219)
.+|||+|+.|.|.|.||+.|||+|.|-|+
T Consensus 108 FVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 108 FVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred cccccccCCcchHHHHHHHHCCeEEEecC
Confidence 49999999999999999999999999754
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=96.63 E-value=0.0035 Score=63.00 Aligned_cols=63 Identities=10% Similarity=0.158 Sum_probs=57.1
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFML 109 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~r 109 (219)
+..+.||+++++.|||.+|++++.|++.+|++|.|+. +|.|.|.. .|...+.+|..+|+.+..
T Consensus 552 ~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-dG~V~i~~----~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 552 IETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-DGTVKIAA----SDGEAAEAAIKMIEGITA 614 (684)
T ss_pred EEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-CeEEEEEE----CcHHHHHHHHHHHHhhhc
Confidence 4668999999999999999999999999999999995 69999987 577899999999998844
No 40
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.53 E-value=0.0044 Score=59.95 Aligned_cols=66 Identities=24% Similarity=0.322 Sum_probs=50.4
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCc---------------------eEEEe---eCCchHHHHHHHHHHHHc-CCC
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADT---------------------KIHIL---GSFANIKIARDSLCSLIL-GSP 200 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~---------------------tV~Ii---G~~~~i~~Ar~aI~~Li~-g~~ 200 (219)
.+|.|||..|.|.|.||..|||+|.|-|+ ..|++ -++|.|+.|-..|+.||. +..
T Consensus 154 FvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 154 FVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIKKAIAVIENLIQSAVS 233 (554)
T ss_pred eeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHHHHHHHHHHHHHhhcc
Confidence 49999999999999999999999999872 23332 456778899999999995 445
Q ss_pred ChhhhHHHHHH
Q 027782 201 AGKVYSKLRAV 211 (219)
Q Consensus 201 ~~~VY~~l~~~ 211 (219)
-...-+.|.+.
T Consensus 234 ~~e~~n~l~~~ 244 (554)
T KOG0119|consen 234 VPEGQNDLKRL 244 (554)
T ss_pred CccccccccHH
Confidence 55555555444
No 41
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.16 E-value=0.018 Score=50.59 Aligned_cols=59 Identities=19% Similarity=0.250 Sum_probs=49.9
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcCce-EEEeeCCc-hHHHHHHHHHHHHcCCCCh
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIADTK-IHILGSFA-NIKIARDSLCSLILGSPAG 202 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V~IiG~~~-~i~~Ar~aI~~Li~g~~~~ 202 (219)
...++|+||++|.+++.|...|++.|.|..+- |.|-|... .+..|.++|+++=+-++-+
T Consensus 153 ~~~i~~lig~~g~~i~~l~~~~~~~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~~ 213 (235)
T PRK04163 153 PVKVPRVIGKKGSMINMLKEETGCDIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHTS 213 (235)
T ss_pred HHHHHhhcCCCChhHhhhhhhhCcEEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhhhhcc
Confidence 35689999999999999999999999999764 88887766 6789999999888665544
No 42
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.99 E-value=0.012 Score=58.92 Aligned_cols=69 Identities=13% Similarity=0.206 Sum_probs=61.7
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHH
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVID 115 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~ 115 (219)
...+.||++.++-+||..|++++.|.+.+|++|.++ ++|+|.|-+ .|...+.+|++.|.++.+.+.+.+
T Consensus 553 i~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-ddGtv~i~~----s~~~~~~~ak~~I~~i~~e~evg~ 621 (692)
T COG1185 553 IETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-DDGTVKIAA----SDGESAKKAKERIEAITREVEVGE 621 (692)
T ss_pred eEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-CCCcEEEEe----cchHHHHHHHHHHHHHHhhccccc
Confidence 466899999999999999999999999999999999 889999997 477899999999999986555433
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=95.92 E-value=0.044 Score=49.90 Aligned_cols=136 Identities=13% Similarity=0.191 Sum_probs=88.7
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEe-CCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKT-RADTPDISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~-~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
..+.+-..--|+++|+.|+.+|.|...+++++.+-...+-=.|.+ +...+....+ -+++|--+-.||+.-+--
T Consensus 50 ~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~i--lk~iip~lee~f~~~~pc---- 123 (390)
T KOG2192|consen 50 LRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEI--LKKIIPTLEEGFQLPSPC---- 123 (390)
T ss_pred EEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHH--HHHHhhhhhhCCCCCCch----
Confidence 446677778899999999999999999999999843333322332 1111222222 346666666666532221
Q ss_pred cCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc-----C--ceEEEe-eCCchHHHHHHHHH
Q 027782 122 LDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA-----D--TKIHIL-GSFANIKIARDSLC 193 (219)
Q Consensus 122 ~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~-----~--~tV~Ii-G~~~~i~~Ar~aI~ 193 (219)
++. -|- | ...-|-|||++|..++.+-+.+.+++.|. + +.|.++ |..+++-..-+.|.
T Consensus 124 ---------e~r---lli--h-qs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~k~v~~~i~~il 188 (390)
T KOG2192|consen 124 ---------ELR---LLI--H-QSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIIL 188 (390)
T ss_pred ---------hhh---hhh--h-hhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCcchHHHHHHHHH
Confidence 111 111 1 23478999999999999999999999886 2 246555 77788877777777
Q ss_pred HHHcCC
Q 027782 194 SLILGS 199 (219)
Q Consensus 194 ~Li~g~ 199 (219)
++|.-+
T Consensus 189 ~~i~e~ 194 (390)
T KOG2192|consen 189 DLISES 194 (390)
T ss_pred HHhhcC
Confidence 777543
No 44
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.90 E-value=0.0078 Score=62.08 Aligned_cols=61 Identities=21% Similarity=0.399 Sum_probs=52.6
Q ss_pred hhhcceecCCCchHHHHHHhhCce-EEEcCc-eEEEee-CCchHHHHHHHHHHHHcCCCChhhh
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTR-IVIADT-KIHILG-SFANIKIARDSLCSLILGSPAGKVY 205 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~-I~V~~~-tV~IiG-~~~~i~~Ar~aI~~Li~g~~~~~VY 205 (219)
..+|.|||++|+|++.|+..||+. |.+.++ +|.|.+ +.+.++.|++.|+.+...-.-|.+|
T Consensus 694 ~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy 757 (891)
T PLN00207 694 EKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIY 757 (891)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEE
Confidence 458999999999999999999999 999875 588887 6677899999999998766667776
No 45
>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=95.75 E-value=0.023 Score=46.63 Aligned_cols=100 Identities=16% Similarity=0.105 Sum_probs=65.3
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhh--
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALL-- 120 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll-- 120 (219)
--..|.+..+|+.+|++|..++.|.+..|-+|.+ |+ -+.|| +.||+.. |+|..-..+.
T Consensus 35 iifvV~~g~vG~~IG~~G~rIk~i~el~gekIdV------Ve-----ys~D~------~~fI~N~---l~PA~V~~V~i~ 94 (141)
T TIGR01952 35 VVFVVKEGEMGAAIGKGGENVKRLEELIGKSIEL------IE-----YSENL------EEFVANK---LAPAEVKNVTVS 94 (141)
T ss_pred EEEEEcCCCccccCCCCchHHHHHHHhcCCeeEE------EE-----cCCCH------HHHHHHc---CCCceEEEEEEE
Confidence 4456777899999999999999998887766655 22 23576 3455543 5554433321
Q ss_pred hcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 121 RLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 121 ~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
+.++-. ...+ ....+-+++.||++|++++-...+||-++-|.
T Consensus 95 ~~~~~~--~a~V--------~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 95 EFNGKK--VAYV--------EVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred cCCCCE--EEEE--------EEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 101111 0111 12244689999999999999999999888554
No 46
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=95.48 E-value=0.02 Score=57.39 Aligned_cols=61 Identities=31% Similarity=0.399 Sum_probs=52.3
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcC-ceEEEeeCC-chHHHHHHHHHHHHcCCCChhhh
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIAD-TKIHILGSF-ANIKIARDSLCSLILGSPAGKVY 205 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~-~tV~IiG~~-~~i~~Ar~aI~~Li~g~~~~~VY 205 (219)
..++-+||++|++++.|-..||+.|.+.+ .+|.|-++. +.++.|++.|+++...-.-|.||
T Consensus 561 dKI~dvIG~gGk~I~~I~eetg~~IdieddGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy 623 (692)
T COG1185 561 DKIRDVIGPGGKTIKAITEETGVKIDIEDDGTVKIAASDGESAKKAKERIEAITREVEVGEVY 623 (692)
T ss_pred HHHhhccCCcccchhhhhhhhCcEEEecCCCcEEEEecchHHHHHHHHHHHHHHhhcccccEE
Confidence 34778999999999999999999999987 469998777 66789999999999766666666
No 47
>PF13014 KH_3: KH domain
Probab=95.33 E-value=0.02 Score=37.03 Aligned_cols=27 Identities=11% Similarity=-0.041 Sum_probs=25.5
Q ss_pred cccchhcCccchhHHHhhcccEEEEEc
Q 027782 52 YSPLKKVWMDIYTPIFEQMKIDIRMNL 78 (219)
Q Consensus 52 v~~lig~wg~i~k~i~e~~~~~i~id~ 78 (219)
+++|||+.|.+++.|++.++++|.|..
T Consensus 2 vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred cCeEECCCChHHHHHHHHhCcEEEECC
Confidence 578999999999999999999999986
No 48
>PRK02821 hypothetical protein; Provisional
Probab=95.18 E-value=0.014 Score=43.29 Aligned_cols=31 Identities=19% Similarity=0.503 Sum_probs=24.2
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcCceEEE
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIADTKIHI 178 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~I 178 (219)
.-+||+|||+|+++++|-.+-.+- .++++.+
T Consensus 40 ~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~l 70 (77)
T PRK02821 40 DDLGKVIGRGGRTATALRTVVAAI---GGRGVRV 70 (77)
T ss_pred hhCcceeCCCCchHHHHHHHHHHh---cCCeEEE
Confidence 348999999999999999876554 6666553
No 49
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=95.06 E-value=0.041 Score=47.31 Aligned_cols=101 Identities=13% Similarity=0.015 Sum_probs=63.2
Q ss_pred EeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhhcC-
Q 027782 45 VNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALLRLD- 123 (219)
Q Consensus 45 I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~~D- 123 (219)
..+-.+-+|..+|+||...+.|.+.+|=+|.+ | .- ..||.. -+.+|++ |..-..+.-.+
T Consensus 80 ~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV------V--e~---s~d~~~-----fI~nal~----Pa~v~~V~~~~~ 139 (190)
T COG0195 80 NVVKIDPVGACIGKRGSRVKAVSEELGEKIDV------V--EW---SEDPAE-----FIKNALA----PAEVLSVNIKED 139 (190)
T ss_pred eecCcCchhhhccCCChHHHHHHHHhCCceEE------E--Ee---CCCHHH-----HHHHhcC----cceEeEEEEEeC
Confidence 34445678999999999999999998833333 2 22 145532 2233332 33333322211
Q ss_pred cceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCce
Q 027782 124 ELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTK 175 (219)
Q Consensus 124 d~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t 175 (219)
|-- ...+ ....+.+++.||++|++.+.+..+||-++.|..-.
T Consensus 140 d~~--~~~v--------~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~~ 181 (190)
T COG0195 140 DGH--VAIV--------VVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETIS 181 (190)
T ss_pred CCc--EEEE--------EECHHHHhhccCcccHHHHHHHHHhCCEEEEEehh
Confidence 110 1111 13456789999999999999999999999987543
No 50
>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=95.03 E-value=0.02 Score=40.14 Aligned_cols=27 Identities=26% Similarity=0.334 Sum_probs=24.7
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEE
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVI 171 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V 171 (219)
.-+|+.||++|++++.++.++|.+|-|
T Consensus 34 ~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 34 DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 458999999999999999999988876
No 51
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.75 E-value=0.03 Score=56.48 Aligned_cols=60 Identities=25% Similarity=0.388 Sum_probs=50.1
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCc-eEEEee-CCchHHHHHHHHHHHHcCCCChhhh
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADT-KIHILG-SFANIKIARDSLCSLILGSPAGKVY 205 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~-tV~IiG-~~~~i~~Ar~aI~~Li~g~~~~~VY 205 (219)
.++.+||++|+|++.|+..||+.|.+.++ +|.+.+ ..+.++.|++.|+.+...-..|.+|
T Consensus 564 kI~~vIG~gg~~ik~I~~~~~~~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~ 625 (693)
T PRK11824 564 KIRDVIGPGGKTIREITEETGAKIDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIY 625 (693)
T ss_pred HHHHHhcCCchhHHHHHHHHCCccccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEE
Confidence 47999999999999999999999999874 588876 5677789999999988655555555
No 52
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=94.65 E-value=0.036 Score=57.37 Aligned_cols=63 Identities=16% Similarity=0.269 Sum_probs=56.9
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccE-EEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKID-IRMNLKARRVELKTRADTPDISNLQKCADFVHAFML 109 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~-i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~r 109 (219)
+..+.||+++++.|||.+|++++.|.+.+|+. |.++. ++.|.|-. .|...+.+|+++|+.+..
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-dg~V~I~a----~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-DGTVKITA----KDLSSLEKSKAIISSLTM 749 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-CeeEEEEe----CCHHHHHHHHHHHHHHhc
Confidence 36689999999999999999999999999999 88885 69999887 578899999999999875
No 53
>PRK00468 hypothetical protein; Provisional
Probab=94.53 E-value=0.02 Score=42.21 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=18.6
Q ss_pred hhcceecCCCchHHHHHHhhCc
Q 027782 146 AIGRLSGKGGKTKFAIENATKT 167 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~ 167 (219)
=+||+|||+|+++++|-.+..+
T Consensus 40 D~GrVIGk~Gr~i~AIRtvv~a 61 (75)
T PRK00468 40 DMGKVIGKQGRIAKAIRTVVKA 61 (75)
T ss_pred hCcceecCCChhHHHHHHHHHH
Confidence 3799999999999999886543
No 54
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.53 E-value=0.094 Score=46.10 Aligned_cols=62 Identities=15% Similarity=0.128 Sum_probs=56.2
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHH
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFM 108 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~ 108 (219)
=+.+.||++.++.|+|..|.+++.|.+.++++|.+.. +|.|-|.+ .++.++.+|..+|+.+.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-NG~VwI~~----~~~~~~~~a~~~I~~~e 207 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-NGRIWIKG----PDEEDEEIAIEAIKKIE 207 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-CcEEEEee----CCHHHHHHHHHHHHHHH
Confidence 3668999999999999999999999999999999985 59999997 57889999999999874
No 55
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=94.36 E-value=0.0033 Score=45.17 Aligned_cols=29 Identities=31% Similarity=0.350 Sum_probs=23.2
Q ss_pred hcceecCCCchHHHHHHhhCceEEEcCce
Q 027782 147 IGRLSGKGGKTKFAIENATKTRIVIADTK 175 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t 175 (219)
.||+|||+|+|+.+||.+++..+.=++..
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~~~~~~~~~~ 68 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVNAAANKHGKR 68 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHHHHHHHT-SS
T ss_pred cceEECCCCeeHHHHHHHHHHHHHhCCCE
Confidence 79999999999999999987765444433
No 56
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.23 E-value=0.12 Score=45.62 Aligned_cols=61 Identities=25% Similarity=0.272 Sum_probs=42.7
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcCce-E-EEeeC---CchHHHHHHHHHHHHcCCCChhhh
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIADTK-I-HILGS---FANIKIARDSLCSLILGSPAGKVY 205 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V-~IiG~---~~~i~~Ar~aI~~Li~g~~~~~VY 205 (219)
..+|.|||+.|.|.+.+|..|+|+|.|-|+. | +.-+. .+...-|...+.-||....--++.
T Consensus 163 NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~adsedki~ 228 (269)
T COG5176 163 NFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEADSEDKIC 228 (269)
T ss_pred ceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhcchhhhHH
Confidence 4599999999999999999999999998753 2 22222 345556666666666544444433
No 57
>PRK01064 hypothetical protein; Provisional
Probab=94.19 E-value=0.024 Score=42.14 Aligned_cols=32 Identities=28% Similarity=0.374 Sum_probs=24.0
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCceEE
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADTKIH 177 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~ 177 (219)
-+||+|||+|+|+++|..+..+--.=.+.+|.
T Consensus 40 D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~ 71 (78)
T PRK01064 40 DIGKIIGKEGRTIKAIRTLLVSVASRNNVKVS 71 (78)
T ss_pred cceEEECCCCccHHHHHHHHHHHHhhCCCEEE
Confidence 37999999999999999976654444444443
No 58
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=94.14 E-value=0.11 Score=48.56 Aligned_cols=157 Identities=19% Similarity=0.165 Sum_probs=112.9
Q ss_pred EEEEeeCCCccccchhcCccchhHHHhhcccEEEEE--------cCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCh
Q 027782 42 FQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMN--------LKARRVELKTRADTPDISNLQKCADFVHAFMLGFDV 113 (219)
Q Consensus 42 ~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id--------~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~ 113 (219)
.-++.+|...-+.+||+.|.++|.+.|++++.|+|- +++++|++. ++|...+||.++|-+-
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~s-----ge~e~~~~A~~~IL~K------ 201 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVS-----GEPEQNMKAVSLILQK------ 201 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEec-----CCHHHHHHHHHHHHHH------
Confidence 368999999999999999999999999999999997 345666665 6899999999999874
Q ss_pred HHHHHhhhcCcceeeeEEe--cccc----cccc--------------------hhhhhhhcceecCCCchHHHHHHhhCc
Q 027782 114 IDAIALLRLDELYVESFEI--KDVK----TLRG--------------------EHLSRAIGRLSGKGGKTKFAIENATKT 167 (219)
Q Consensus 114 e~A~~Ll~~Dd~~~e~i~I--~dv~----~~~~--------------------~~~~R~~gRIIGk~G~t~~~IE~~Tg~ 167 (219)
+-+ |+-+-..+.+ .++. +.++ -.+.-..|---|.+|.+.-+|--.||.
T Consensus 202 -----i~e-Dpqs~scln~sya~vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~ 275 (402)
T KOG2191|consen 202 -----IQE-DPQSGSCLNISYANVSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGA 275 (402)
T ss_pred -----hhc-CCcccceeccchhcccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeeccccc
Confidence 344 3333222332 1211 0000 011234566667788888888899999
Q ss_pred eEEEc---------CceEEEeeCCchHHHHHHHHHHHHcCCCChhhhHHHHHHHHHH
Q 027782 168 RIVIA---------DTKIHILGSFANIKIARDSLCSLILGSPAGKVYSKLRAVTARL 215 (219)
Q Consensus 168 ~I~V~---------~~tV~IiG~~~~i~~Ar~aI~~Li~g~~~~~VY~~l~~~~~~~ 215 (219)
.+.+. +..+.++|..-.+..|-.++.++...+.....-.+++..+..+
T Consensus 276 l~~itq~l~~m~g~gy~~n~~g~~ls~~aa~g~L~~~~~~a~t~~a~~~~qs~a~~a 332 (402)
T KOG2191|consen 276 LIAITQALNTMAGYGYNTNILGLGLSILAAEGVLAAKVASANTAAAAANLQSYASEA 332 (402)
T ss_pred ceeecccccccccccccccccchhhhhhhhhhHHHHhhcccCcccchhhHHHHHHHh
Confidence 77764 2237778888888889999999998887777777777766544
No 59
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=93.68 E-value=2.5 Score=35.89 Aligned_cols=137 Identities=12% Similarity=0.049 Sum_probs=94.7
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhh
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALL 120 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll 120 (219)
....+.+++.-+-.|-...+.+.+.|....|++|.+....+.|.|++ +...+.-+..-|..+ |
T Consensus 26 g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~~i~I~g-----~k~~~~~i~~~i~~~------------l 88 (210)
T PF14611_consen 26 GDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRSENRIRITG-----TKSTAEYIEASINEI------------L 88 (210)
T ss_pred ceeEEEecchheeeeecCCchHHHHHHHhcCceEEEecCCcEEEEEc-----cHHHHHHHHHHHHHH------------H
Confidence 34556777888888889999999999778899999999999999986 344555555555544 2
Q ss_pred hcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCce--EEEe-----eCCchHHHHHHHHH
Q 027782 121 RLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTK--IHIL-----GSFANIKIARDSLC 193 (219)
Q Consensus 121 ~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t--V~Ii-----G~~~~i~~Ar~aI~ 193 (219)
.++..+.|++..+... +.....+ --....+..|+.+|+|+|...++. +.|. -..+++..|++.+.
T Consensus 89 --~~i~~~~i~l~~~~~~----~~~~~~~--~~~~~~l~~i~~~t~~~ie~~~~~~~~~i~~~~~~~~~~~~~~a~RlL~ 160 (210)
T PF14611_consen 89 --SNIRTEEIDLSPIISK----HSEKKNS--QFTPDLLEEIQKLTNVYIEKNPDGNKLKISWLASPENEKRADRAKRLLL 160 (210)
T ss_pred --hhcEEEEEecchhhhh----hcccccc--cccHHHHHHHHHHHcEEEEECCCCCeEEEEEEeeccccchHHHHHHHHH
Confidence 4566677887765421 1110111 124568899999999999988754 4443 45677789999888
Q ss_pred HHHcCCCCh
Q 027782 194 SLILGSPAG 202 (219)
Q Consensus 194 ~Li~g~~~~ 202 (219)
-.+...+|.
T Consensus 161 ~a~~~~~~~ 169 (210)
T PF14611_consen 161 WALDYNPHS 169 (210)
T ss_pred HhccCCccc
Confidence 777544443
No 60
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=93.16 E-value=0.31 Score=42.21 Aligned_cols=66 Identities=30% Similarity=0.332 Sum_probs=55.0
Q ss_pred hhhhcceecCCCchHHHHHHhhCceEEEcCce--EEEeeC---CchH--HHHHHHHHHHHcCCCChhhhHHHH
Q 027782 144 SRAIGRLSGKGGKTKFAIENATKTRIVIADTK--IHILGS---FANI--KIARDSLCSLILGSPAGKVYSKLR 209 (219)
Q Consensus 144 ~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t--V~IiG~---~~~i--~~Ar~aI~~Li~g~~~~~VY~~l~ 209 (219)
..+.|=+||+.|.+++.||..++|.+.++.++ |.|..+ .+++ .-|++.|..+=.|=++...+.-|+
T Consensus 16 k~R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe~A~~LL~ 88 (194)
T COG1094 16 KDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPEKALKLLE 88 (194)
T ss_pred chhheeeecccccchHHHHhhcCeEEEEECCCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHHHHHHHhc
Confidence 45689999999999999999999999999754 777654 4665 589999988889999988877664
No 61
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=92.99 E-value=0.061 Score=52.81 Aligned_cols=130 Identities=14% Similarity=0.097 Sum_probs=84.3
Q ss_pred eeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCC-CCHHHHHHHHHHHHHHHcCCChHHHHH
Q 027782 40 VQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADT-PDISNLQKCADFVHAFMLGFDVIDAIA 118 (219)
Q Consensus 40 ~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t-~dp~~i~KA~d~I~Ai~rGF~~e~A~~ 118 (219)
.-.-++.+|..-+..++|+.|..+++|.+.++.++.++.+ .+.=+++... +-|...-+|+..+-. +
T Consensus 67 ~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e--d~g~e~~~~~~~~p~~v~~a~a~~~~-----------~ 133 (608)
T KOG2279|consen 67 DIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE--DVGDERVLLISGFPVQVCKAKAAIHQ-----------I 133 (608)
T ss_pred heeeeEeecccceeeeeccccCCcchhhcccccceecCcc--cCCcccchhhccCCCCCChHHHHHHH-----------H
Confidence 4456789999999999999999999999999999988754 2221221110 112222223222221 2
Q ss_pred hhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcCc------eEEEeeCCchH-HHHHHH
Q 027782 119 LLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADT------KIHILGSFANI-KIARDS 191 (219)
Q Consensus 119 Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~------tV~IiG~~~~i-~~Ar~a 191 (219)
+++ ...+ +.+.-.++|..+||+|++|.+.+.|+.-++++|.+..+ ....++..... ..|+..
T Consensus 134 ~~~-~~pv----------k~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~ 202 (608)
T KOG2279|consen 134 LTE-NTPV----------SEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHL 202 (608)
T ss_pred Hhc-CCcc----------cccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhh
Confidence 233 2221 22344678999999999999999999999999999854 23344444444 366655
Q ss_pred HH
Q 027782 192 LC 193 (219)
Q Consensus 192 I~ 193 (219)
+.
T Consensus 203 ~~ 204 (608)
T KOG2279|consen 203 IL 204 (608)
T ss_pred hh
Confidence 43
No 62
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=92.55 E-value=0.078 Score=39.38 Aligned_cols=19 Identities=37% Similarity=0.571 Sum_probs=17.1
Q ss_pred hcceecCCCchHHHHHHhh
Q 027782 147 IGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~T 165 (219)
.||+|||+|+|+++|-.+-
T Consensus 41 ~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred ccceecCCChhHHHHHHHH
Confidence 7999999999999998753
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=92.08 E-value=0.14 Score=51.65 Aligned_cols=62 Identities=11% Similarity=0.167 Sum_probs=54.6
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFML 109 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~r 109 (219)
..+.||+++++.+||.+|++++.|.+.+|+.+.++. +|.|.+.. .+...+.+|+++|+.+..
T Consensus 556 ~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d-~G~v~i~~----~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 556 ETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED-DGTVKIAA----TDGEAAEAAKERIEGITA 617 (693)
T ss_pred eeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-CceEEEEc----ccHHHHHHHHHHHHHhcc
Confidence 457789999999999999999999999999888864 69998886 477899999999999864
No 64
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=91.63 E-value=0.15 Score=34.60 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=21.1
Q ss_pred hcceecCCCchHHHHHHhhCceE
Q 027782 147 IGRLSGKGGKTKFAIENATKTRI 169 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I 169 (219)
.|++||++|++++.++.+++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 69999999999999999999665
No 65
>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=91.47 E-value=0.11 Score=37.91 Aligned_cols=26 Identities=35% Similarity=0.327 Sum_probs=23.1
Q ss_pred hcceecCCCchHHHHHHhhCceEEEc
Q 027782 147 IGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
.|++||++|+|+.+||-+++..+.-.
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCeEECCCCccHHHHHHHHHHHHhhc
Confidence 59999999999999999998777654
No 66
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=91.06 E-value=0.36 Score=44.93 Aligned_cols=65 Identities=31% Similarity=0.252 Sum_probs=50.2
Q ss_pred hhhhhhhcceecCCCchHHHHHHhhCceEEEcC---c--eEEE-eeCCchHHHHHHHHHHHHc--C-CCChhhh
Q 027782 141 EHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD---T--KIHI-LGSFANIKIARDSLCSLIL--G-SPAGKVY 205 (219)
Q Consensus 141 ~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~---~--tV~I-iG~~~~i~~Ar~aI~~Li~--g-~~~~~VY 205 (219)
...+...|-|||+.|+|++-||+-|+|.|.+.- + .|.| .+..++|..|.+-|..+|. + +-|-+.|
T Consensus 62 ~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r~s~p~thf 135 (345)
T KOG2814|consen 62 LVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRKSFPITHF 135 (345)
T ss_pred hhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhhcCchhhh
Confidence 344567999999999999999999999999962 2 2444 4667788899999999984 4 5555544
No 67
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=90.39 E-value=1.1 Score=40.03 Aligned_cols=51 Identities=18% Similarity=0.304 Sum_probs=42.9
Q ss_pred hcceecCCCchHHHHHHhhCceEEEcCc-eEEEeeCCch-HHHHHHHHHHHHc
Q 027782 147 IGRLSGKGGKTKFAIENATKTRIVIADT-KIHILGSFAN-IKIARDSLCSLIL 197 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I~V~~~-tV~IiG~~~~-i~~Ar~aI~~Li~ 197 (219)
+=|+||++|..++.+...|+|+|.|.-+ .|.+=|..+. ...|-.||.++=.
T Consensus 157 VpRvig~~~sm~~~l~~~~~~~I~VG~NG~IWV~~~~~~~e~~~~~aI~~ie~ 209 (239)
T COG1097 157 VPRVIGKKGSMLNMLKEKTGCEIIVGQNGRIWVDGENESLEELAIEAIRKIER 209 (239)
T ss_pred cceEecCCCcHHHHhhhhcCeEEEEecCCEEEecCCCcchHHHHHHHHHHHhh
Confidence 4579999999999999999999999876 5888888885 5688888877654
No 68
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=89.40 E-value=0.52 Score=45.67 Aligned_cols=52 Identities=33% Similarity=0.381 Sum_probs=43.0
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCc----eEEEeeCCchHHHHHHHHHHHHc
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADT----KIHILGSFANIKIARDSLCSLIL 197 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~----tV~IiG~~~~i~~Ar~aI~~Li~ 197 (219)
.+|.+||++|..++-||+-|+++|.+... .|.|-|.-.--..|+.+|..++.
T Consensus 57 mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 57 MVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred hhheeeccCcchhhhhhcccceeEEEeccCceeEEEEechHHHHHHHHhhHhhhhh
Confidence 49999999999999999999999999743 36666766555688888888874
No 69
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=87.25 E-value=1.7 Score=39.91 Aligned_cols=64 Identities=9% Similarity=0.104 Sum_probs=53.4
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEc-----CCceEEEEeCCCCCCHHHHHHHHHHHHHH
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNL-----KARRVELKTRADTPDISNLQKCADFVHAF 107 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~-----~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai 107 (219)
-..+-+|.||++--|-|||+.|+-++.|...+|++|.+|. .++-++|. +.-..++.|+.+++--
T Consensus 313 PitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitIt-----GTqdQIqnAQYLlQn~ 381 (390)
T KOG2192|consen 313 PITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITIT-----GTQDQIQNAQYLLQNS 381 (390)
T ss_pred ceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEe-----ccHHHHhhHHHHHHHH
Confidence 4788999999999999999999999999999999999985 23444454 4567899999887754
No 70
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=86.02 E-value=1.7 Score=40.75 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=44.3
Q ss_pred hcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCchHHHHHHHHH
Q 027782 147 IGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFANIKIARDSLC 193 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~i~~Ar~aI~ 193 (219)
.-.+.|..|.+++.||...|+.|...|..+.++|....+..|+.++.
T Consensus 26 ~~~l~G~~~~~l~l~e~~~gv~i~~rG~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 26 LVALFGPTDTNLSLLEIALGVSIVARGEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred hhhhcCCCCccHHHHHHHhCcEEEeCCceEEEEechHHHHHHHHHHh
Confidence 45689999999999999999999999999999999889999999998
No 71
>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=84.43 E-value=0.9 Score=31.67 Aligned_cols=37 Identities=11% Similarity=-0.060 Sum_probs=33.0
Q ss_pred eeEEEEeeCCCccccchhcCccchhHHHhhcccEEEE
Q 027782 40 VQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRM 76 (219)
Q Consensus 40 ~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~i 76 (219)
.....+.||++-++..+|+.|...+.+.+.++.+|.+
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 3678899999999999999999999999999876654
No 72
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=83.26 E-value=2.8 Score=37.18 Aligned_cols=78 Identities=12% Similarity=0.065 Sum_probs=55.0
Q ss_pred CCCCcCCCCCCCCCceeEEEEeeC------CCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCC-CCHHHH
Q 027782 25 PLFEPLKAHEMSDGRVQFQKVNVP------PHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADT-PDISNL 97 (219)
Q Consensus 25 ~~~~p~~~~~~~~~~~~~~~I~IP------~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t-~dp~~i 97 (219)
|.|-+.+.-..+. ..+-+++|| .+-+|.|+|.-|.+.+.|++.++++|-|-.. ++|. -|... ..|..+
T Consensus 134 p~fv~p~dy~rps--k~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~-gsvK--egk~ssd~p~~~ 208 (269)
T COG5176 134 PRFVLPNDYIRPS--KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS-GSVK--EGKISSDTPESL 208 (269)
T ss_pred CcccCCccccCcc--cccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc-cccc--cCcccccCchhh
Confidence 5666665554444 233455555 3578999999999999999999999999854 4443 22222 348888
Q ss_pred HHHHHHHHHH
Q 027782 98 QKCADFVHAF 107 (219)
Q Consensus 98 ~KA~d~I~Ai 107 (219)
..|.+.+..+
T Consensus 209 ~N~e~~lhcL 218 (269)
T COG5176 209 KNAEAVLHCL 218 (269)
T ss_pred hhhHHhHHHH
Confidence 9998888776
No 73
>COG1159 Era GTPase [General function prediction only]
Probab=81.77 E-value=3.1 Score=38.29 Aligned_cols=57 Identities=25% Similarity=0.312 Sum_probs=37.4
Q ss_pred HHHHHhhhcCcc-eeeeEEecccccccchhh----------hhhhcceecCCCchHHH--------HHHhhCceEEE
Q 027782 114 IDAIALLRLDEL-YVESFEIKDVKTLRGEHL----------SRAIGRLSGKGGKTKFA--------IENATKTRIVI 171 (219)
Q Consensus 114 e~A~~Ll~~Dd~-~~e~i~I~dv~~~~~~~~----------~R~~gRIIGk~G~t~~~--------IE~~Tg~~I~V 171 (219)
|+++.+++ |++ +.-.++|.+++...++.+ ...+|-|||++|..++. ||.+.+|++.+
T Consensus 198 Ek~~~~l~-eElPhsv~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L 273 (298)
T COG1159 198 EKLLLLLR-EELPHSVAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYL 273 (298)
T ss_pred HHHHHhcc-cccCceEEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEE
Confidence 78888888 665 655666666553211111 13799999999987765 56666766655
No 74
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=80.66 E-value=1.1 Score=39.22 Aligned_cols=50 Identities=26% Similarity=0.352 Sum_probs=36.0
Q ss_pred hcceecCCCchHHHHHHhhCceEEEcCce-EEE---eeCCchH------HHHHHHHHHHH
Q 027782 147 IGRLSGKGGKTKFAIENATKTRIVIADTK-IHI---LGSFANI------KIARDSLCSLI 196 (219)
Q Consensus 147 ~gRIIGk~G~t~~~IE~~Tg~~I~V~~~t-V~I---iG~~~~i------~~Ar~aI~~Li 196 (219)
.||+||++|+|..+||-+++..+.-.+.+ ..+ +|.|.-= ..|.++-....
T Consensus 102 ~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRerR~e~L~~LA~~~A~rV~ 161 (208)
T COG1847 102 AGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRERRKETLIKLAERAAERVL 161 (208)
T ss_pred hhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999998886543 444 4555332 35555555554
No 75
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=79.74 E-value=4.8 Score=39.57 Aligned_cols=85 Identities=13% Similarity=0.137 Sum_probs=59.0
Q ss_pred CCCCCCCcCCCCCCCCCceeEEEEeeCC------CccccchhcCccchhHHHhhcccEEEEEcCCceEE---EEeCC---
Q 027782 22 PLKPLFEPLKAHEMSDGRVQFQKVNVPP------HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVE---LKTRA--- 89 (219)
Q Consensus 22 ~~~~~~~p~~~~~~~~~~~~~~~I~IP~------~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~---I~~~~--- 89 (219)
+..|.|+|..+-..+. .-.-+++||- +-+|.|||--|.+.|.|++.+|++|.|--+ |+|. .++.+
T Consensus 121 k~nP~fkpP~DYk~p~--~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGk-gSvkEgk~~~~d~~~ 197 (554)
T KOG0119|consen 121 KLNPGFKPPADYKPPA--KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGK-GSVKEGKGRSDDLSY 197 (554)
T ss_pred HhCcCCCCCcccCccc--ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEecc-ccccccccCCccccc
Confidence 3468899988877664 2334566664 568999999999999999999999999752 2221 11110
Q ss_pred ------------CCCCHHHHHHHHHHHHHHHc
Q 027782 90 ------------DTPDISNLQKCADFVHAFML 109 (219)
Q Consensus 90 ------------~t~dp~~i~KA~d~I~Ai~r 109 (219)
...+-..|.+|..+|+.+..
T Consensus 198 ~~~~~epLH~~Isadt~eki~~Ai~vienli~ 229 (554)
T KOG0119|consen 198 IPKENEPLHCLISADTQEKIKKAIAVIENLIQ 229 (554)
T ss_pred ccccccceeEEEecchHHHHHHHHHHHHHHHH
Confidence 11345678888888887753
No 76
>PRK12704 phosphodiesterase; Provisional
Probab=79.09 E-value=5.9 Score=38.92 Aligned_cols=65 Identities=11% Similarity=-0.014 Sum_probs=50.9
Q ss_pred ceeEEEEeeCC-CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHH
Q 027782 39 RVQFQKVNVPP-HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAF 107 (219)
Q Consensus 39 ~~~~~~I~IP~-~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai 107 (219)
+.....|.+|. +--|-|||+.|..++.|+..+|+.+-||..-..|.|.+ .||.-=.-|+.-+..+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~----~~~~rre~a~~~l~~l 273 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSG----FDPIRREIARLALEKL 273 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCCCCeEEEec----CChhhHHHHHHHHHHH
Confidence 45566799999 56689999999999999999999999997767777765 5776645555544443
No 77
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=77.58 E-value=3.8 Score=38.19 Aligned_cols=94 Identities=14% Similarity=0.163 Sum_probs=58.3
Q ss_pred CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHh--hhcCccee
Q 027782 50 HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIAL--LRLDELYV 127 (219)
Q Consensus 50 ~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~L--l~~Dd~~~ 127 (219)
+=+|+.+|..|.-++.+.+.++ ...|+|-. -..||. .||. .-++|.+...+ ++ ++-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~--------ge~Idiv~--~s~d~~------~fi~---nal~Pa~v~~v~i~~-~~~-- 300 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELN--------GEKIDIIE--YSDDPA------EFIA---NALSPAKVISVEVLD-EDK-- 300 (341)
T ss_pred CcceeeECCCCchHHHHHHHhC--------CCeEEEEE--cCCCHH------HHHH---HhcCCceEEEEEEEc-CCC--
Confidence 3478899999999999987762 24454332 124552 2322 23556554443 23 221
Q ss_pred eeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC
Q 027782 128 ESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 128 e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
..+.+. ......+.-||++|+|.+-.-.+||.+|-|..
T Consensus 301 ~~~~v~--------V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVV--------VPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEE--------EChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 112221 12335788899999999999999999998863
No 78
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=76.99 E-value=7 Score=38.35 Aligned_cols=62 Identities=11% Similarity=-0.016 Sum_probs=50.8
Q ss_pred ceeEEEEeeCC-CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 39 RVQFQKVNVPP-HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 39 ~~~~~~I~IP~-~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
+.....|.+|. +--|-|||+.|..++.|+..+|+.+-||..-..|.|.+ .||+-=.-|+--+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddtp~~v~ls~----fdp~rreia~~~l 264 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDTPEAVILSG----FDPVRREIARMAL 264 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCCCCeEEecC----CchHHHHHHHHHH
Confidence 46667799999 56689999999999999999999999998778888876 7887655555433
No 79
>PRK15494 era GTPase Era; Provisional
Probab=76.47 E-value=5.4 Score=36.63 Aligned_cols=58 Identities=16% Similarity=0.158 Sum_probs=34.6
Q ss_pred HHHHHhhhcCcc-eeeeEEecccccccchhh----------hhhhcceecCCCchHHH--------HHHhhCceEEEc
Q 027782 114 IDAIALLRLDEL-YVESFEIKDVKTLRGEHL----------SRAIGRLSGKGGKTKFA--------IENATKTRIVIA 172 (219)
Q Consensus 114 e~A~~Ll~~Dd~-~~e~i~I~dv~~~~~~~~----------~R~~gRIIGk~G~t~~~--------IE~~Tg~~I~V~ 172 (219)
|..+..|+ +++ |.-.+.|..++...++.+ ...++-|||++|+.++. ||.+.||++.+.
T Consensus 242 e~~~~~~~-~EiP~~~~v~i~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 242 EQLFLNLQ-KELPYKLTVQTEKWEDLKDKSVKINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred HHHHhhCC-cccCceEEEEEEEEEEcCCCeEEEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 56667777 554 443344433332111111 24789999999998765 577777777653
No 80
>PRK00106 hypothetical protein; Provisional
Probab=76.44 E-value=7.6 Score=38.44 Aligned_cols=62 Identities=11% Similarity=-0.019 Sum_probs=51.2
Q ss_pred ceeEEEEeeCC-CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHH
Q 027782 39 RVQFQKVNVPP-HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFV 104 (219)
Q Consensus 39 ~~~~~~I~IP~-~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I 104 (219)
+.....|.+|+ +--|-|||+.|..++.|+..+|+.+-||..-..|.|.+ .||+-=.-|+--+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~v~lS~----fdpvRReiAr~~l 285 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDTPEVVVLSG----FDPIRREIARMTL 285 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCCCCeEEEeC----CChHHHHHHHHHH
Confidence 46667799999 56689999999999999999999999998888888876 7887655555433
No 81
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=76.04 E-value=5.2 Score=37.92 Aligned_cols=94 Identities=11% Similarity=-0.020 Sum_probs=57.4
Q ss_pred CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhhcCcceeee
Q 027782 50 HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALLRLDELYVES 129 (219)
Q Consensus 50 ~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~~Dd~~~e~ 129 (219)
+=+|+.+|..|.-++.|.+.++ ...|+|-. -..||. .||.. -++|.+...+.-.++-- .
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~--------gEkIDvI~--~s~D~~------~fI~N---al~Pa~V~~V~i~~~~~--~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELN--------GENIDCIE--YSNVPE------IFIAR---ALAPAIISSVKIEEEEK--K 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhC--------CCeEEEEE--cCCCHH------HHHHH---hCCCceeeEEEEcCCCc--E
Confidence 4478899999999999988762 24455332 114552 33332 24555444331102211 1
Q ss_pred EEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 130 FEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 130 i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
+.+. ......++-||++|++.+-.-.+||.+|-|.
T Consensus 310 ~~V~--------V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~ 344 (374)
T PRK12328 310 AIVT--------LLSDQKSKAIGKNGINIRLASMLTGYEIELN 344 (374)
T ss_pred EEEE--------EChHHhhhhhcCCChhHHHHHHHhCCEEEEE
Confidence 1211 1123468889999999999999999999986
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=74.07 E-value=5.3 Score=38.89 Aligned_cols=94 Identities=11% Similarity=0.079 Sum_probs=56.9
Q ss_pred ccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhhcCcceeeeE
Q 027782 51 RYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALLRLDELYVESF 130 (219)
Q Consensus 51 Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~~Dd~~~e~i 130 (219)
=+|+.+|..|.-++.|.+.++ ...|+|-. -..||. .-+.+| ++|.....+.-+++- ..+
T Consensus 246 pvga~vG~~G~ri~~i~~el~--------ge~Idiv~--~s~d~~-----~fi~na----l~pa~v~~v~~~~~~--~~~ 304 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELG--------GEKIDIIL--WSDDPA-----QFIINA----LSPAEVSSVVVDEDE--HSA 304 (470)
T ss_pred hhHccCCCCCchHHHHHHHhC--------CCeEEEEE--cCCCHH-----HHHHHh----CCCCEEEEEEEeCCC--CEE
Confidence 378889999999999987762 34455433 113552 222333 344443333210211 122
Q ss_pred EecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC
Q 027782 131 EIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 131 ~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
.+. ......+.-|||+|+|++-...+||.+|-|..
T Consensus 305 ~v~--------V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 305 DVV--------VPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEE--------ECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 221 11234678899999999999999999999864
No 83
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=73.68 E-value=2.3 Score=42.54 Aligned_cols=52 Identities=21% Similarity=0.241 Sum_probs=45.4
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCch-HHHHHHHHHHHHc
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFAN-IKIARDSLCSLIL 197 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~-i~~Ar~aI~~Li~ 197 (219)
.+.-+||++|..+|-||..||+.-.|++.|+.|...... .+.||+-|.-++.
T Consensus 607 k~~~lIGp~G~~~kki~~EtGai~~vDe~t~~i~A~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 607 KRATLIGPGGVLKKKIEVETGAISQVDEGTFSIFAPTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred hhheeecCccceeeeEeeeccceeeecCceEEEEecCHHHHHHHHHHHHHHhc
Confidence 356799999999999999999999999999999866554 4799999998884
No 84
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=73.56 E-value=7.6 Score=34.10 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=20.4
Q ss_pred hhhcceecCCCchHHHH--------HHhhCceEEE
Q 027782 145 RAIGRLSGKGGKTKFAI--------ENATKTRIVI 171 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~I--------E~~Tg~~I~V 171 (219)
+.+|-|||++|+.++.| |.+.||++.+
T Consensus 231 s~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l 265 (270)
T TIGR00436 231 SQKKIIIGKNGSMIKAIGIAARKDILELFDCDVFL 265 (270)
T ss_pred CceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 47899999999987764 5666666654
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=73.37 E-value=7.1 Score=36.76 Aligned_cols=94 Identities=14% Similarity=0.129 Sum_probs=58.5
Q ss_pred CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHh-h-hcCccee
Q 027782 50 HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIAL-L-RLDELYV 127 (219)
Q Consensus 50 ~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~L-l-~~Dd~~~ 127 (219)
+=+|+.+|..|.-++.+.+.++ ...|+|-. -..|| ..||.- -++|.....+ + + ++--
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~--------gekIdiv~--~s~d~------~~fi~n---al~Pa~v~~v~i~~-~~~~- 303 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELK--------GEKIDIID--WSEDP------AEFVAN---ALSPAKVVSVEVDD-EEEK- 303 (362)
T ss_pred CchheeECCCChhHHHHHHHhC--------CCeEEEEE--cCCCH------HHHHHH---hCCCceEEEEEEEc-CCCc-
Confidence 3478899999999999987762 24454332 11455 233332 3556554443 1 2 2211
Q ss_pred eeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC
Q 027782 128 ESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 128 e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
.+.+. .....++.-||++|+|.+.--.+||.+|-|..
T Consensus 304 -~~~v~--------V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 304 -AARVV--------VPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred -EEEEE--------EChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 12211 12345788999999999999999999998874
No 86
>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=72.42 E-value=0.46 Score=34.20 Aligned_cols=33 Identities=18% Similarity=0.300 Sum_probs=24.6
Q ss_pred hhhcceecCCCchHHHHHHhhCceEE-EcCceEE
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIV-IADTKIH 177 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~-V~~~tV~ 177 (219)
...|.+||++|++++.|....+-.+. +.+..|+
T Consensus 34 ~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~ 67 (78)
T PF07650_consen 34 SQPGIVIGKKGSNIKKIREELRKELEKLLNKKVF 67 (78)
T ss_dssp SSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEE
T ss_pred CCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEE
Confidence 35899999999999999887766664 4444444
No 87
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=70.91 E-value=6.2 Score=39.66 Aligned_cols=61 Identities=10% Similarity=0.167 Sum_probs=52.1
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHc
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFML 109 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~r 109 (219)
..+.+|+....-|||..|...|.|+..+|....+| ++++.|-. .++.+..+|++||..|..
T Consensus 599 ~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD--e~t~~i~A----~~~~am~~Ak~~I~~i~~ 659 (760)
T KOG1067|consen 599 ETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD--EGTFSIFA----PTQAAMEEAKEFIDGIIK 659 (760)
T ss_pred eEEeecchhhheeecCccceeeeEeeeccceeeec--CceEEEEe----cCHHHHHHHHHHHHHHhc
Confidence 34889999999999999999999999999766666 57787775 588999999999998743
No 88
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=69.50 E-value=8.8 Score=37.27 Aligned_cols=94 Identities=11% Similarity=0.100 Sum_probs=59.2
Q ss_pred CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHh--hhcCccee
Q 027782 50 HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIAL--LRLDELYV 127 (219)
Q Consensus 50 ~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~L--l~~Dd~~~ 127 (219)
+=+|+.+|..|.-++.|.+.++ ...|.|-. -..||. .||. .-++|.+...+ .+ ++--
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~--------gEkIDVI~--ys~Dp~------~fI~---NaLsPA~V~~V~i~~-~~~k- 335 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELR--------GEKIDVIR--WSPDPA------TYIA---NALSPARVDEVRLVD-PEGR- 335 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhC--------CCeEEEEE--cCCCHH------HHHH---HhcCCceeeEEEEEc-CCCc-
Confidence 4589999999999999988762 34454332 124552 3333 23566554443 22 2211
Q ss_pred eeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC
Q 027782 128 ESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 128 e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
.+.+. ......++-|||+|+|++---.+||.+|-|..
T Consensus 336 -~a~V~--------V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 336 -HAHVL--------VPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred -EEEEE--------EChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 12211 11234788899999999999999999998875
No 89
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=65.36 E-value=4.8 Score=37.61 Aligned_cols=154 Identities=16% Similarity=0.096 Sum_probs=105.1
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCc-eEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHh
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKAR-RVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIAL 119 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~-~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~L 119 (219)
=+..+.+|..-++.+-|..|-.++.|..++...|.--+..+ -|... |+-+..+.+|+.=|.+-+.-|..-.|..-
T Consensus 26 vt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~v----Tg~~edv~~aRrei~saaeH~~l~~~s~s 101 (394)
T KOG2113|consen 26 VTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPV----TGRHEDVRRARREIPSAAEHFGLIRASRS 101 (394)
T ss_pred cceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCccee----ccCchhHHHHhhcCccccceeeeeeeccc
Confidence 34568899888899999999999999888888876544322 34333 35667888999888776655665555554
Q ss_pred hhcCcc--eeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEc---CceEEE-eeCCch-HHHHH-HH
Q 027782 120 LRLDEL--YVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIA---DTKIHI-LGSFAN-IKIAR-DS 191 (219)
Q Consensus 120 l~~Dd~--~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~---~~tV~I-iG~~~~-i~~Ar-~a 191 (219)
+. .+. +-++-+...+. ..+-|.+|.+.|..|.+++.|+.-|+++|.-- +..|.. -|-..+ ++.|| .=
T Consensus 102 ~S-gg~~~~s~s~qt~sy~----svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~e 176 (394)
T KOG2113|consen 102 FS-GGTNGASASGQTTSYV----SVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCE 176 (394)
T ss_pred cc-CCCccccccCCCceee----eccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccc
Confidence 44 222 11122222222 24478999999999999999999999999754 334655 476666 67777 56
Q ss_pred HHHHH---cCCCChh
Q 027782 192 LCSLI---LGSPAGK 203 (219)
Q Consensus 192 I~~Li---~g~~~~~ 203 (219)
||+-+ .|.+|.+
T Consensus 177 ie~ta~~ra~~i~d~ 191 (394)
T KOG2113|consen 177 IEQTAVTRAGQIHDT 191 (394)
T ss_pred hhhhhhhhhhccccC
Confidence 66665 2666665
No 90
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=63.89 E-value=5.7 Score=32.39 Aligned_cols=26 Identities=27% Similarity=0.410 Sum_probs=23.0
Q ss_pred hhcceecCCCchHHHHHHhhCceEEE
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVI 171 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V 171 (219)
..|..||++|+.++.|+++.|-+|-|
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdV 67 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIEL 67 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEE
Confidence 47999999999999999999866655
No 91
>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=58.44 E-value=65 Score=26.76 Aligned_cols=28 Identities=29% Similarity=0.261 Sum_probs=24.7
Q ss_pred hhcceecCCCchHHHHHHhhCceEEEcC
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
.-|++||++|.+++.|-.-||-.-.|.-
T Consensus 86 KPG~ViGk~g~~~reI~~~tgW~p~vvR 113 (145)
T cd02410 86 KPGLVIGKGGSTLREITRETGWAPKVVR 113 (145)
T ss_pred CCeEEEecCchhHHHHHHHhCCeeEEEe
Confidence 4699999999999999999998877753
No 92
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=54.86 E-value=17 Score=34.15 Aligned_cols=76 Identities=5% Similarity=-0.055 Sum_probs=57.0
Q ss_pred CCCCcCCCCCCCCCceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEc---CCceEEEEeCCCCCCHHHHHHHH
Q 027782 25 PLFEPLKAHEMSDGRVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNL---KARRVELKTRADTPDISNLQKCA 101 (219)
Q Consensus 25 ~~~~p~~~~~~~~~~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~---~~~~V~I~~~~~t~dp~~i~KA~ 101 (219)
+.+-+.+..+.+...-.+..+.+|+.-++-|+|..|.+.+.|++.++++|-+-. +...|.+.. .....+++|.
T Consensus 41 ~p~~~~dv~~~~~~~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~~i~i~~----~~~~~V~~a~ 116 (345)
T KOG2814|consen 41 MPGDTVDVEDDAGAKDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIG----ISRNCVIQAL 116 (345)
T ss_pred CCCChHHhhhccccccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEee----hhHHHHHHHH
Confidence 445555555555544566779999999999999999999999999999998843 446666665 4566777776
Q ss_pred HHH
Q 027782 102 DFV 104 (219)
Q Consensus 102 d~I 104 (219)
+=|
T Consensus 117 ~Ri 119 (345)
T KOG2814|consen 117 ERI 119 (345)
T ss_pred HHH
Confidence 544
No 93
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=53.50 E-value=53 Score=33.92 Aligned_cols=124 Identities=15% Similarity=0.131 Sum_probs=81.2
Q ss_pred eeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEc---CCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHH
Q 027782 40 VQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNL---KARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDA 116 (219)
Q Consensus 40 ~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~---~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A 116 (219)
...-++.+-+.-..+++|+.+.-...|++.+.+.+.+-. ..+.|.+.. .-..+.+|.+.+.-+..++
T Consensus 346 n~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~-----~~~~~~ka~~~v~~~~~ei----- 415 (753)
T KOG2208|consen 346 NENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITG-----VSANDEKAVEDVEKIIAEI----- 415 (753)
T ss_pred ceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEec-----cccchhHHHHHHHHHHHhh-----
Confidence 344556777888899999999988889999999888853 334455543 3456777777776552211
Q ss_pred HHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhC-ceEEEcCc-----eEEEeeCCchHHHH
Q 027782 117 IALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATK-TRIVIADT-----KIHILGSFANIKIA 188 (219)
Q Consensus 117 ~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg-~~I~V~~~-----tV~IiG~~~~i~~A 188 (219)
++ ...-+.+. -+.+...||||.+|..+.+|..-+| ++|..+.+ .+.+-|.+..+..+
T Consensus 416 ---~n--~~~~~~~~----------iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~~~~~~~~~~~~dv~~~ 478 (753)
T KOG2208|consen 416 ---LN--SIVKEEVQ----------IPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNSSDMVTIRGISKDVEKS 478 (753)
T ss_pred ---hc--ccccceee----------cCccchhhhhccccccHHHHHhhcCcEEEecCCCCcccccceEeccccccchh
Confidence 11 01111122 3456689999999999999999999 55555532 25555666665543
No 94
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=51.90 E-value=12 Score=26.92 Aligned_cols=35 Identities=23% Similarity=0.277 Sum_probs=23.7
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCchH
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFANI 185 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~i 185 (219)
-..|..||++|..++.|++..+ |..|-++...++.
T Consensus 17 d~vG~~iG~~G~rik~i~~~L~------gekIdvV~~s~d~ 51 (69)
T PF13184_consen 17 DPVGACIGKKGSRIKAISEELN------GEKIDVVEYSDDP 51 (69)
T ss_dssp -HHHHHH-CCCCCHHHHHHHTT------T-EEEEEE--SSH
T ss_pred CcceecCccccHHHHHHHHHhC------CCeEEEEEcCCCH
Confidence 4589999999999999999995 5555555544443
No 95
>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=50.34 E-value=14 Score=30.33 Aligned_cols=26 Identities=27% Similarity=0.434 Sum_probs=22.9
Q ss_pred hhcceecCCCchHHHHHHhhCceEEE
Q 027782 146 AIGRLSGKGGKTKFAIENATKTRIVI 171 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~I~V 171 (219)
-.|..||++|..++.|+++.|-+|-|
T Consensus 43 ~vG~~IG~~G~rIk~i~el~gekIdV 68 (141)
T TIGR01952 43 EMGAAIGKGGENVKRLEELIGKSIEL 68 (141)
T ss_pred CccccCCCCchHHHHHHHhcCCeeEE
Confidence 48999999999999999999866655
No 96
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=50.29 E-value=19 Score=25.03 Aligned_cols=67 Identities=9% Similarity=0.162 Sum_probs=45.9
Q ss_pred EEEeeCCCccccchhcCcc--chhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCC
Q 027782 43 QKVNVPPHRYSPLKKVWMD--IYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFD 112 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~--i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~ 112 (219)
..+.++.+++..+.|..-. -...+.+++|+.+..+..++.+.+..... = ..++...|+|..++|.+.
T Consensus 2 ~~i~~~~~~i~~llG~~i~~~ei~~~L~~lg~~~~~~~~~~~~~v~~P~~--R-~Di~~~~DliEei~r~~G 70 (71)
T smart00874 2 RTITLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTLEVTVPSY--R-FDILIEADLIEEVARIYG 70 (71)
T ss_pred cEEEecHHHHHHHHCCCCCHHHHHHHHHHCCCeEEecCCCCeEEEECCCC--c-cccCcccHHHHHHHHHhC
Confidence 3577888888888886543 23345577888887644346677765422 2 478889999999987653
No 97
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=49.84 E-value=12 Score=37.05 Aligned_cols=39 Identities=15% Similarity=0.033 Sum_probs=35.1
Q ss_pred eEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC
Q 027782 41 QFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK 79 (219)
Q Consensus 41 ~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~ 79 (219)
+.--+.+|++.++.++|+.|..++.|++.+|++|.+-+.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 346799999999999999999999999999999998654
No 98
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=49.83 E-value=14 Score=32.14 Aligned_cols=98 Identities=12% Similarity=0.097 Sum_probs=63.6
Q ss_pred cchhHHHhhcccEEEEEcCCceEEEEeCCC-CCCHHHHHHHHHHHHH-HHcCCChHHHHHhhhcCcceeeeEEecccccc
Q 027782 61 DIYTPIFEQMKIDIRMNLKARRVELKTRAD-TPDISNLQKCADFVHA-FMLGFDVIDAIALLRLDELYVESFEIKDVKTL 138 (219)
Q Consensus 61 ~i~k~i~e~~~~~i~id~~~~~V~I~~~~~-t~dp~~i~KA~d~I~A-i~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~ 138 (219)
+..+.|-+.+|.-+.++ +..+..-+.-- .+-.+...-++.++++ +..||++++|.++.. . .+.-.-. +...
T Consensus 125 ~~v~~lf~~~G~~~~v~--E~~~~~~talsgsgPA~~~~~~~al~~~~v~~Gl~~~~A~~lv~-~-~~~G~a~---l~~~ 197 (245)
T TIGR00112 125 ALVLALFKAVGEVVELP--EALMDAVTALSGSGPAYVFLFIEALADAGVKQGLPRELALELAA-Q-TVKGAAK---LLEE 197 (245)
T ss_pred HHHHHHHHhCCCEEEEC--HHHcchHHhhccCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH-H-HHHHHHH---HHHh
Confidence 56677888889999887 34554333211 1333434444555544 568999999999875 2 2111111 1112
Q ss_pred cchhhhhhhcceecCCCchHHHHHHhh
Q 027782 139 RGEHLSRAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 139 ~~~~~~R~~gRIIGk~G~t~~~IE~~T 165 (219)
++.++...+.++.-++|-|...|+.+-
T Consensus 198 ~~~~~~~l~~~v~spgGtT~~gl~~Le 224 (245)
T TIGR00112 198 SGEHPALLKDQVTSPGGTTIAGLAVLE 224 (245)
T ss_pred cCCCHHHHHHcCCCCcHHHHHHHHHHH
Confidence 457899999999999999999998874
No 99
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=47.80 E-value=16 Score=30.94 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=22.5
Q ss_pred cceecCCCchHHHHHHhhCceEEEc
Q 027782 148 GRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 148 gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
|.-||++|++++.+++..|-+|-|-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEE
Confidence 8899999999999999998877764
No 100
>PRK12705 hypothetical protein; Provisional
Probab=47.29 E-value=25 Score=34.64 Aligned_cols=59 Identities=7% Similarity=-0.028 Sum_probs=46.2
Q ss_pred ceeEEEEeeCC-CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHH
Q 027782 39 RVQFQKVNVPP-HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCA 101 (219)
Q Consensus 39 ~~~~~~I~IP~-~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~ 101 (219)
+.....|.+|. +--|-|||+.|..++.++..+|+.+-||..-+.|.|.+ .||.--..|+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddtp~~V~ls~----fdp~rreia~ 255 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDTPEAVVISS----FNPIRREIAR 255 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCCccchhhcc----cCccchHHHH
Confidence 45566788898 55689999999999999999999999998777777665 5555433333
No 101
>PRK00089 era GTPase Era; Reviewed
Probab=45.97 E-value=16 Score=32.20 Aligned_cols=28 Identities=25% Similarity=0.388 Sum_probs=21.7
Q ss_pred hhhcceecCCCchHHH--------HHHhhCceEEEc
Q 027782 145 RAIGRLSGKGGKTKFA--------IENATKTRIVIA 172 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~--------IE~~Tg~~I~V~ 172 (219)
..++-|||++|++++. ||.+.||+|.+.
T Consensus 236 ~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 236 SQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred CceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 4689999999998775 567778777653
No 102
>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=43.95 E-value=14 Score=28.61 Aligned_cols=23 Identities=17% Similarity=0.169 Sum_probs=18.8
Q ss_pred hhcceecCCCchHHHHHHhhCce
Q 027782 146 AIGRLSGKGGKTKFAIENATKTR 168 (219)
Q Consensus 146 ~~gRIIGk~G~t~~~IE~~Tg~~ 168 (219)
.-|.|||++|++++.|+......
T Consensus 71 rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 71 RPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred CCCcccCCchHHHHHHHHHHHHH
Confidence 46999999999999988765544
No 103
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=43.30 E-value=16 Score=36.06 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=26.8
Q ss_pred hhhhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 143 LSRAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 143 ~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
....++.+|||+|++++.||+..|.+|-|.
T Consensus 493 pe~~i~~vigk~g~~i~~ie~klgi~I~v~ 522 (604)
T COG1855 493 PEKYIPKVIGKGGKRIKEIEKKLGIKIDVK 522 (604)
T ss_pred CHHHhhHHhhcccchHHHHHHHhCCceEEE
Confidence 345689999999999999999999999885
No 104
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=43.24 E-value=8 Score=29.78 Aligned_cols=62 Identities=15% Similarity=0.178 Sum_probs=38.2
Q ss_pred HHHHHHHH-HHcCCChHHHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhh
Q 027782 99 KCADFVHA-FMLGFDVIDAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 99 KA~d~I~A-i~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~T 165 (219)
-+..++++ +..|++.++|.++.. . .+.-. ..+..-++.++...+.++.-++|-|.+.|+.+-
T Consensus 23 ~~eal~~a~v~~Gl~~~~A~~lv~-~-t~~G~---a~ll~~~~~~~~~l~~~v~tPgG~T~~gl~~L~ 85 (107)
T PF14748_consen 23 FIEALADAAVAQGLPREEARKLVA-Q-TFIGA---AKLLEESGRSPAELRDEVTTPGGTTIAGLEVLE 85 (107)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHH-H-HHHHH---HHHHHHCSS-HHHHHHHHS-TTSHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH-H-HHHHH---HHHHHccCCCHHHHhhhccCCCCcHHHHHHHHH
Confidence 34445544 558999999999875 1 11101 111112456899999999999999999998764
No 105
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=43.11 E-value=52 Score=27.73 Aligned_cols=56 Identities=13% Similarity=0.162 Sum_probs=46.0
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcC--ceEEEeeCCchHHHHHHHHHHHHcCCC
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIAD--TKIHILGSFANIKIARDSLCSLILGSP 200 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~--~tV~IiG~~~~i~~Ar~aI~~Li~g~~ 200 (219)
...--|...+|...+.|-...||+|.+.. +.+.|.|+...++.+...|..++....
T Consensus 35 ~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~~~~i~I~g~k~~~~~i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 35 DEFFLLLTGNGRILENLAARNGAKIEVSRSENRIRITGTKSTAEYIEASINEILSNIR 92 (210)
T ss_pred hheeeeecCCchHHHHHHHhcCceEEEecCCcEEEEEccHHHHHHHHHHHHHHHhhcE
Confidence 34566788889998888666799999964 579999999999999999999886543
No 106
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=42.25 E-value=65 Score=28.90 Aligned_cols=46 Identities=15% Similarity=0.206 Sum_probs=40.7
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCC
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRA 89 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~ 89 (219)
.-+.||+.++--+||+.+...+.|.++++|.|-+- .+|.|=|.+.+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG-~NG~IWV~~~~ 193 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVG-QNGRIWVDGEN 193 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEe-cCCEEEecCCC
Confidence 45899999999999999999999999999999776 56999998743
No 107
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=42.23 E-value=31 Score=31.29 Aligned_cols=38 Identities=16% Similarity=0.038 Sum_probs=32.2
Q ss_pred eeEEEEeeCCC------ccccchhcCccchhHHHhhcccEEEEE
Q 027782 40 VQFQKVNVPPH------RYSPLKKVWMDIYTPIFEQMKIDIRMN 77 (219)
Q Consensus 40 ~~~~~I~IP~~------Rv~~lig~wg~i~k~i~e~~~~~i~id 77 (219)
.-+.+|.||-+ -+|-|.|-.|.+.+.|++.++|+|-|-
T Consensus 91 k~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 91 KLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred eEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 44566777765 589999999999999999999999885
No 108
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=39.76 E-value=42 Score=34.68 Aligned_cols=53 Identities=23% Similarity=0.273 Sum_probs=46.0
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcC-----ceEEEeeCCchHHHHHHHHHHHHc
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIAD-----TKIHILGSFANIKIARDSLCSLIL 197 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~-----~tV~IiG~~~~i~~Ar~aI~~Li~ 197 (219)
....=++|++|.+++-|++.++|.|.+.. +.+.+-|...+++-|.+.++..+.
T Consensus 356 ~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ 413 (753)
T KOG2208|consen 356 EELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVSANDEKAVEDVEKIIA 413 (753)
T ss_pred HhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccccchhHHHHHHHHHHH
Confidence 45677999999999999999999999974 358889999999988888887774
No 109
>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=38.79 E-value=17 Score=26.84 Aligned_cols=28 Identities=11% Similarity=0.203 Sum_probs=20.5
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
..-|.+||++|+.++.|.....-..-+.
T Consensus 39 arPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 39 TRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3469999999999998877554444443
No 110
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=37.52 E-value=64 Score=21.81 Aligned_cols=30 Identities=13% Similarity=0.028 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHHHHHcCCChHHHHHhh
Q 027782 91 TPDISNLQKCADFVHAFMLGFDVIDAIALL 120 (219)
Q Consensus 91 t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll 120 (219)
..++..+...+.+..+...||+++++.++|
T Consensus 38 ~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 38 LYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred ecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 357789999999999999999999999886
No 111
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=37.25 E-value=17 Score=39.63 Aligned_cols=58 Identities=21% Similarity=0.204 Sum_probs=49.9
Q ss_pred cchhhhhhhcceecCCCchHHHHHHhhCceEEEcC----c----eEEEeeCCchHHHHHHHHHHHH
Q 027782 139 RGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD----T----KIHILGSFANIKIARDSLCSLI 196 (219)
Q Consensus 139 ~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~----~----tV~IiG~~~~i~~Ar~aI~~Li 196 (219)
..+.+.-+..|+||++|.++.++-..||+.|-|.. + ++.+-|..+..++|...|.-+|
T Consensus 1343 k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i 1408 (2131)
T KOG4369|consen 1343 KGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPI 1408 (2131)
T ss_pred ccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcccccee
Confidence 34667778999999999999999999999999862 2 6888899999999998887666
No 112
>PRK13764 ATPase; Provisional
Probab=37.23 E-value=23 Score=35.60 Aligned_cols=31 Identities=29% Similarity=0.344 Sum_probs=27.3
Q ss_pred hhhhhhcceecCCCchHHHHHHhhCceEEEc
Q 027782 142 HLSRAIGRLSGKGGKTKFAIENATKTRIVIA 172 (219)
Q Consensus 142 ~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~ 172 (219)
...+-++.+|||+|+++..||+..|.+|-|.
T Consensus 487 ~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~ 517 (602)
T PRK13764 487 VPEKDIPKVIGKGGKRIKKIEKKLGIDIDVR 517 (602)
T ss_pred EChhhhhHHhccCcchHHHHHHHhCCceEEE
Confidence 3455689999999999999999999999885
No 113
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=36.79 E-value=1.2e+02 Score=19.95 Aligned_cols=30 Identities=10% Similarity=0.300 Sum_probs=23.0
Q ss_pred cchhHHHhhccc-EEEEEcCCceEEEEeCCC
Q 027782 61 DIYTPIFEQMKI-DIRMNLKARRVELKTRAD 90 (219)
Q Consensus 61 ~i~k~i~e~~~~-~i~id~~~~~V~I~~~~~ 90 (219)
.+.+.|...-|+ .+.+|..++.+.|.....
T Consensus 15 ~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~ 45 (62)
T PF00403_consen 15 KVEKALSKLPGVKSVKVDLETKTVTVTYDPD 45 (62)
T ss_dssp HHHHHHHTSTTEEEEEEETTTTEEEEEESTT
T ss_pred HHHHHHhcCCCCcEEEEECCCCEEEEEEecC
Confidence 455667777676 599999999999998543
No 114
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=36.49 E-value=31 Score=30.78 Aligned_cols=69 Identities=10% Similarity=0.113 Sum_probs=52.0
Q ss_pred EEEeeCCCccccchhcCccchhHHH----hhccc-EEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHH
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIF----EQMKI-DIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAI 117 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~----e~~~~-~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~ 117 (219)
..|.|=..|=|.+||+.|..++.|. +.++. .++||. .+|+. .+..+.+-|..+-.++-+|+++-.|+
T Consensus 53 ~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~~v~I~i----~EV~~----peL~A~lvA~~IA~qLErrv~FRRA~ 124 (233)
T COG0092 53 TRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKENVQINI----EEVKK----PELDAQLVAESIAQQLERRVSFRRAM 124 (233)
T ss_pred eEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCCCceEEE----EEcCC----CCcCHHHHHHHHHHHHHcccHHHHHH
Confidence 3455556788999999999877654 45666 466653 35554 46678999999999999999999998
Q ss_pred Hh
Q 027782 118 AL 119 (219)
Q Consensus 118 ~L 119 (219)
+-
T Consensus 125 k~ 126 (233)
T COG0092 125 KR 126 (233)
T ss_pred HH
Confidence 53
No 115
>PRK12548 shikimate 5-dehydrogenase; Provisional
Probab=36.35 E-value=90 Score=27.89 Aligned_cols=117 Identities=15% Similarity=0.258 Sum_probs=57.6
Q ss_pred cchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHH-HcCCCh-----HHHHHhhhcCcceeeeEEecc
Q 027782 61 DIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAF-MLGFDV-----IDAIALLRLDELYVESFEIKD 134 (219)
Q Consensus 61 ~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai-~rGF~~-----e~A~~Ll~~Dd~~~e~i~I~d 134 (219)
.+....-+.+|+...+- .+++ +|..+..+-..+++. .+|+++ +.++.+++ ++ .+
T Consensus 26 ~ihn~~f~~~gl~~~Y~----~~~v-------~~~~l~~~~~~~~~~~~~G~nVT~P~K~~v~~~ld--~~-------~~ 85 (289)
T PRK12548 26 AMYNYSFQKAGLDYAYL----AFDI-------PVDKVPDAIKAIKTFNMRGANVTMPCKSEAAKYMD--EL-------SP 85 (289)
T ss_pred HHHHHHHHHcCCCEEEE----EEec-------CHHHHHHHHHHHHHCCCCEEEECccCHHHHHHHhh--cC-------CH
Confidence 34455556667654442 2222 234444444444443 256654 67777775 11 11
Q ss_pred cccc--cchhhhhhhcceecCCCchHHHHHHhhCceEEEcCceEEEeeCCchHHHHHHHHHHHH-cCCC
Q 027782 135 VKTL--RGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIADTKIHILGSFANIKIARDSLCSLI-LGSP 200 (219)
Q Consensus 135 v~~~--~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~tV~IiG~~~~i~~Ar~aI~~Li-~g~~ 200 (219)
.... .-|-+.+.-||++|-+=...=.+..+....+.+.++++.|+|. + -+||-+...|. .|..
T Consensus 86 ~A~~iGavNTi~~~~g~l~G~NTD~~G~~~~l~~~~~~~~~k~vlI~GA--G-GagrAia~~La~~G~~ 151 (289)
T PRK12548 86 AARIIGAVNTIVNDDGKLTGHITDGLGFVRNLREHGVDVKGKKLTVIGA--G-GAATAIQVQCALDGAK 151 (289)
T ss_pred HHHHhCceeEEEeECCEEEEEecCHHHHHHHHHhcCCCcCCCEEEEECC--c-HHHHHHHHHHHHCCCC
Confidence 1110 1122323357888876555444444433223456777888888 2 55555555555 3543
No 116
>PRK07680 late competence protein ComER; Validated
Probab=35.82 E-value=30 Score=30.33 Aligned_cols=96 Identities=13% Similarity=0.061 Sum_probs=58.1
Q ss_pred cchhHHHhhcccEEEEEcCCceEEEEeCCCCCC--HHHHHHHHHHHHHHH--cCCChHHHHHhhhcCcceeeeEEecccc
Q 027782 61 DIYTPIFEQMKIDIRMNLKARRVELKTRADTPD--ISNLQKCADFVHAFM--LGFDVIDAIALLRLDELYVESFEIKDVK 136 (219)
Q Consensus 61 ~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~d--p~~i~KA~d~I~Ai~--rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~ 136 (219)
+..+.|.+..|....++.+ .....+ ..++. .+...-..-|+.+-. .||+.++|.+++. +.+..+.++ .
T Consensus 142 ~~~~~ll~~~G~~~~i~e~--~~~~~~-~l~gs~pa~~~~~~~al~~~~~~~~Gl~~~~a~~~~~--~~~~G~~~l---~ 213 (273)
T PRK07680 142 QKLERLFSNISTPLVIEED--ITRVSS-DIVSCGPAFFSYLLQRFIDAAVEETNISKEEATTLAS--EMLIGMGKL---L 213 (273)
T ss_pred HHHHHHHHcCCCEEEEChH--hcchhh-hhccchHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHH--HHHHHHHHH---H
Confidence 4456677788877777633 222211 11122 233333334554444 4999999998875 222111221 1
Q ss_pred cccchhhhhhhcceecCCCchHHHHHHh
Q 027782 137 TLRGEHLSRAIGRLSGKGGKTKFAIENA 164 (219)
Q Consensus 137 ~~~~~~~~R~~gRIIGk~G~t~~~IE~~ 164 (219)
..++.|+...+.++.-++|-|.+.++.+
T Consensus 214 ~~~~~~~~~l~~~v~spgG~T~~gl~~l 241 (273)
T PRK07680 214 EKGLYTLPTLQEKVCVKGGITGEGIKVL 241 (273)
T ss_pred HhcCCCHHHHHHhCCCCChhHHHHHHHH
Confidence 1245799999999999999999998876
No 117
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=35.59 E-value=25 Score=35.12 Aligned_cols=57 Identities=12% Similarity=0.244 Sum_probs=45.5
Q ss_pred hhhcceecCCCchHHHHHHhhCceEEEcCc-----eEEE-eeCCchHHHHHHHHHHHHcCCCC
Q 027782 145 RAIGRLSGKGGKTKFAIENATKTRIVIADT-----KIHI-LGSFANIKIARDSLCSLILGSPA 201 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~~-----tV~I-iG~~~~i~~Ar~aI~~Li~g~~~ 201 (219)
..+-.++|+.|.+++.|+..|+.+|.+.+. ++-+ .|-..++.-|+.+++..+..+.+
T Consensus 77 e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~p 139 (608)
T KOG2279|consen 77 EAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTENTP 139 (608)
T ss_pred cceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhcCCc
Confidence 457789999999999999999999999854 3444 45777888999988887754433
No 118
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=35.00 E-value=34 Score=28.95 Aligned_cols=31 Identities=10% Similarity=-0.030 Sum_probs=25.8
Q ss_pred EeeCCCccccchhcCccchhHHHhhcccEEEE
Q 027782 45 VNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRM 76 (219)
Q Consensus 45 I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~i 76 (219)
+.|.+.. |..||+||++.+.+++.+|-+|++
T Consensus 65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~Vev 95 (166)
T PRK06418 65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRV 95 (166)
T ss_pred EEEeCCC-cccccccchHHHHHHHHhCCcEEE
Confidence 3444455 999999999999999999888877
No 119
>PRK04056 Maf-like protein; Reviewed
Probab=34.51 E-value=59 Score=27.52 Aligned_cols=37 Identities=19% Similarity=0.172 Sum_probs=28.1
Q ss_pred eEEEcCceEE-----EeeCCchHHHHHHHHHHHHcCCCChhhhH
Q 027782 168 RIVIADTKIH-----ILGSFANIKIARDSLCSLILGSPAGKVYS 206 (219)
Q Consensus 168 ~I~V~~~tV~-----IiG~~~~i~~Ar~aI~~Li~g~~~~~VY~ 206 (219)
.++|..+||. |+|.+.+.+.|++.+..| .|+.|. ||+
T Consensus 62 ~~vI~aDTvV~~~g~ilgKP~~~~eA~~~L~~l-sg~~h~-V~T 103 (180)
T PRK04056 62 CNLLVADSVVSCGNKILRKAKDKEEAREMLKLQ-SGNEIS-VLT 103 (180)
T ss_pred CEEEEeCEEEEECCEEecCCCCHHHHHHHHHHH-CCCcEE-EEE
Confidence 4667666643 689999999999988766 788885 653
No 120
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=33.23 E-value=1.4e+02 Score=23.06 Aligned_cols=48 Identities=23% Similarity=0.255 Sum_probs=36.2
Q ss_pred CchHHHHHHhhCceEEEcCc------------eEEEe--eCCchHHHHHHHHHHHHcCCCCh
Q 027782 155 GKTKFAIENATKTRIVIADT------------KIHIL--GSFANIKIARDSLCSLILGSPAG 202 (219)
Q Consensus 155 G~t~~~IE~~Tg~~I~V~~~------------tV~Ii--G~~~~i~~Ar~aI~~Li~g~~~~ 202 (219)
+.....++.+.||+++|-+. -|..+ +....|+.|-+.+..++.+.|+.
T Consensus 52 ~~~~~~~~~l~~c~vvi~~~IG~~a~~~L~~~gI~~~~~~~~~~v~eal~~l~~~~~~~~~~ 113 (119)
T TIGR02663 52 DKIAPKIEALKDCAILYCLAIGGPAAAKVVAAKIHPIKVNEPESISELLERLQKMLKGNPPP 113 (119)
T ss_pred chHHHHHHHhCCCcEEEEhhcCccHHHHHHHcCCeeEecCCCccHHHHHHHHHHHHcCCCCH
Confidence 44556689999999999743 23333 66667999999999999998885
No 121
>PF08383 Maf_N: Maf N-terminal region; InterPro: IPR013592 This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression [], in erythroid differentiation [], and in differentiation of the neuroretina [].
Probab=32.67 E-value=30 Score=22.08 Aligned_cols=14 Identities=36% Similarity=0.430 Sum_probs=11.3
Q ss_pred HcCCChHHHHHhhh
Q 027782 108 MLGFDVIDAIALLR 121 (219)
Q Consensus 108 ~rGF~~e~A~~Ll~ 121 (219)
+.|++||||...|-
T Consensus 20 ~l~LtpEDAvEaLi 33 (35)
T PF08383_consen 20 ALGLTPEDAVEALI 33 (35)
T ss_pred hcCCCHHHHHHHHh
Confidence 46899999998763
No 122
>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=31.90 E-value=33 Score=25.24 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=16.3
Q ss_pred hhhcceecCCCchHHHHHHhh
Q 027782 145 RAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 145 R~~gRIIGk~G~t~~~IE~~T 165 (219)
...|.+||++|++++.+....
T Consensus 47 ~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 47 ERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred CCCCceECCCchhHHHHHHHH
Confidence 356999999999888776543
No 123
>PRK06928 pyrroline-5-carboxylate reductase; Reviewed
Probab=31.21 E-value=1.5e+02 Score=26.13 Aligned_cols=98 Identities=12% Similarity=0.082 Sum_probs=61.7
Q ss_pred ccchhHHHhhcccEEEEEcCCceEEEEeCC-CCCCHHHHHHHHHHHHH-HHc-CCChHHHHHhhhcCcceeeeEEecccc
Q 027782 60 MDIYTPIFEQMKIDIRMNLKARRVELKTRA-DTPDISNLQKCADFVHA-FML-GFDVIDAIALLRLDELYVESFEIKDVK 136 (219)
Q Consensus 60 g~i~k~i~e~~~~~i~id~~~~~V~I~~~~-~t~dp~~i~KA~d~I~A-i~r-GF~~e~A~~Ll~~Dd~~~e~i~I~dv~ 136 (219)
.+..+.|.+.+|.-..++. ..+..-+.- -.+-.|-..-+.-|+.| +.. ||+.++|.++.. . .+.-.-++ .
T Consensus 144 ~~~v~~l~~~~G~~~~v~E--~~~d~~tal~gsgPA~~~~~~~al~~a~~~~ggl~~~~a~~l~~-~-~~~G~a~l---~ 216 (277)
T PRK06928 144 KSRLEETLSHFSHVMTIRE--ENMDIASNLTSSSPGFIAAIFEEFAEAAVRNSSLSDEEAFQFLN-F-ALAGTGKL---L 216 (277)
T ss_pred HHHHHHHHHhCCCEEEEch--hhCceeeeeecCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHH-H-HHHHHHHH---H
Confidence 3466778888999998873 444433311 11233434444455554 334 699999999875 2 11111111 1
Q ss_pred cccchhhhhhhcceecCCCchHHHHHHh
Q 027782 137 TLRGEHLSRAIGRLSGKGGKTKFAIENA 164 (219)
Q Consensus 137 ~~~~~~~~R~~gRIIGk~G~t~~~IE~~ 164 (219)
..++.|+...+.++.-++|-|+..|+.+
T Consensus 217 ~~~~~~p~~l~~~v~spgGtT~~gl~~l 244 (277)
T PRK06928 217 VEEDYTFSGTIERVATKGGITAEGAEVI 244 (277)
T ss_pred HccCCCHHHHHHhCCCCChHHHHHHHHH
Confidence 1246789999999999999999999876
No 124
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=30.95 E-value=34 Score=32.19 Aligned_cols=54 Identities=24% Similarity=0.317 Sum_probs=45.2
Q ss_pred hhhhhhhcceecCCCchHHHHHHhhCceEEEc--Cc-eEE-EeeCCchHHHHHHHHHH
Q 027782 141 EHLSRAIGRLSGKGGKTKFAIENATKTRIVIA--DT-KIH-ILGSFANIKIARDSLCS 194 (219)
Q Consensus 141 ~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~--~~-tV~-IiG~~~~i~~Ar~aI~~ 194 (219)
..+.+.++-+.|++|-+++++...|.+||+=. ++ .+. +-|.+++++.||+=|..
T Consensus 31 ~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~~edv~~aRrei~s 88 (394)
T KOG2113|consen 31 EVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGRHEDVRRARREIPS 88 (394)
T ss_pred ecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccCchhHHHHhhcCcc
Confidence 45578899999999999999999999999865 32 244 46999999999997765
No 125
>PRK06476 pyrroline-5-carboxylate reductase; Reviewed
Probab=30.64 E-value=88 Score=27.03 Aligned_cols=101 Identities=13% Similarity=0.117 Sum_probs=60.0
Q ss_pred cchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHH-HHcCCChHHHHHhhhcCcceeeeEEeccccccc
Q 027782 61 DIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHA-FMLGFDVIDAIALLRLDELYVESFEIKDVKTLR 139 (219)
Q Consensus 61 ~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~A-i~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~~ 139 (219)
+..+.|.+..|..+.+..+ .....-+.--..-.+...-...++.+ ...||++++|.+++. ..+.-..++ +...+
T Consensus 134 ~~~~~l~~~lG~~~~~~~e-~~~d~~~a~~s~~a~~~~~~~~~~~~~~~~Gl~~~~a~~~~~--~~~~G~~~l--~~~~~ 208 (258)
T PRK06476 134 PFVAALFDALGTAVECDSE-EEYDLLAAASALMATYFGILETATGWLEEQGLKRQKARAYLA--PLFASLAQD--AVRST 208 (258)
T ss_pred HHHHHHHHhcCCcEEECCh-HhccceeehhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH--HHHHHHHHH--HHhcC
Confidence 3566777888888876533 33332221111223333333344333 457999999998875 222111111 01124
Q ss_pred chhhhhhhcceecCCCchHHHHHHhhC
Q 027782 140 GEHLSRAIGRLSGKGGKTKFAIENATK 166 (219)
Q Consensus 140 ~~~~~R~~gRIIGk~G~t~~~IE~~Tg 166 (219)
+.++...+.++.-++|-|.+.|+.+-.
T Consensus 209 ~~~~~~l~~~v~spgGtT~~gl~~le~ 235 (258)
T PRK06476 209 KTDFSALSREFSTKGGLNEQVLNDFSR 235 (258)
T ss_pred CCCHHHHHHhCCCCCchHHHHHHHHHH
Confidence 578889999999999999999998743
No 126
>PRK13764 ATPase; Provisional
Probab=30.60 E-value=47 Score=33.49 Aligned_cols=41 Identities=17% Similarity=0.043 Sum_probs=36.2
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcC
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLK 79 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~ 79 (219)
....-.|.||..-++.++|+.|..++.|++++|+.|++-+.
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 34567799999999999999999999999999999988653
No 127
>PRK02821 hypothetical protein; Provisional
Probab=29.73 E-value=77 Score=23.40 Aligned_cols=34 Identities=15% Similarity=0.012 Sum_probs=28.7
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhccc
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKI 72 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~ 72 (219)
......+.+.+.=+|-+||+.|.+.+.|......
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 4567899999999999999999999988765544
No 128
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=29.72 E-value=1e+02 Score=20.98 Aligned_cols=30 Identities=7% Similarity=0.104 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 92 PDISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 92 ~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
.++.++...+.+..+...||++++...+++
T Consensus 38 y~~~~l~~l~~i~~l~~~g~~l~~i~~~l~ 67 (67)
T cd04764 38 YTDEDIELLKKIKTLLEKGLSIKEIKEILN 67 (67)
T ss_pred eCHHHHHHHHHHHHHHHCCCCHHHHHHHhC
Confidence 578899999999999999999999988763
No 129
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=29.00 E-value=21 Score=30.29 Aligned_cols=96 Identities=13% Similarity=0.082 Sum_probs=53.8
Q ss_pred cchhHHHhhcccEEEEEcCCceEEEEeCCCC-CCHHHHHHHHHHHHH-HHcCCChHHHHHhhhcCcceeeeEEecccccc
Q 027782 61 DIYTPIFEQMKIDIRMNLKARRVELKTRADT-PDISNLQKCADFVHA-FMLGFDVIDAIALLRLDELYVESFEIKDVKTL 138 (219)
Q Consensus 61 ~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t-~dp~~i~KA~d~I~A-i~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~ 138 (219)
+....|.+.+|....++.+ ....-+.--. +-++...-+.-++++ ...||+.++|.+++. ..+....++ + .
T Consensus 147 ~~v~~lf~~~G~~~~~~e~--~~~~~~a~~gs~pa~~~~~~~a~~~~~~~~Gl~~~~a~~~~~--~~~~g~~~~--~--~ 218 (245)
T PRK07634 147 ETLQLILKGIGTSQLCTEE--EVHQLTAVTGSAPAFLYYFAESLIEATKSYGVDEETAKHLVI--QMISGSASM--L--E 218 (245)
T ss_pred HHHHHHHHhCCCEEEECHH--HcchHHhhhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHH--HHHHHHHHH--H--h
Confidence 4455566666777766532 2222111111 112222233333333 347999999999875 221111111 1 1
Q ss_pred cchhhhhhhcceecCCCchHHHHHHh
Q 027782 139 RGEHLSRAIGRLSGKGGKTKFAIENA 164 (219)
Q Consensus 139 ~~~~~~R~~gRIIGk~G~t~~~IE~~ 164 (219)
++.++...+.++.=++|-|...+..+
T Consensus 219 ~~~~~~~l~~~v~spgG~T~~gl~~l 244 (245)
T PRK07634 219 QTQDPANLREQVTTPGGSTAEGLKAL 244 (245)
T ss_pred CCCCHHHHHHhCCCCChHHHHHHHHh
Confidence 24578889999999999999998764
No 130
>PRK00258 aroE shikimate 5-dehydrogenase; Reviewed
Probab=28.59 E-value=80 Score=27.91 Aligned_cols=102 Identities=23% Similarity=0.238 Sum_probs=53.8
Q ss_pred HHHHHHHHHHHHHH-HcCCCh-----HHHHHhhhcCcceeeeEEecccccc--cchhhhhhhcceecCCCchHHHHHHhh
Q 027782 94 ISNLQKCADFVHAF-MLGFDV-----IDAIALLRLDELYVESFEIKDVKTL--RGEHLSRAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 94 p~~i~KA~d~I~Ai-~rGF~~-----e~A~~Ll~~Dd~~~e~i~I~dv~~~--~~~~~~R~~gRIIGk~G~t~~~IE~~T 165 (219)
|..+..+-..+++. .+|+++ +.++.+++ . +.+.... .-|-+.+.-|+++|-+=...=.+..+.
T Consensus 44 ~~~l~~~~~~~~~~~~~G~nVT~P~K~~~~~~~d--~-------~~~~A~~igavNtv~~~~g~l~G~NTD~~G~~~~l~ 114 (278)
T PRK00258 44 PEDLEDAVKGFFALGGRGANVTVPFKEAAFALAD--E-------LSERARLIGAVNTLVLEDGRLIGDNTDGIGFVRALE 114 (278)
T ss_pred HHHHHHHHHHHHhCCCCEEEECcCCHHHHHHHhh--c-------CCHHHHHhCCceEEEeeCCEEEEEcccHHHHHHHHH
Confidence 34555555555554 367654 56777764 1 1111110 112333445778887655544444443
Q ss_pred C-ceEEEcCceEEEeeCCchHHHHHHHHHHHH-cCCCChhhhHH
Q 027782 166 K-TRIVIADTKIHILGSFANIKIARDSLCSLI-LGSPAGKVYSK 207 (219)
Q Consensus 166 g-~~I~V~~~tV~IiG~~~~i~~Ar~aI~~Li-~g~~~~~VY~~ 207 (219)
. ..+.+.+++|.|+|.- .+||.++..|. .|-.+=+|++.
T Consensus 115 ~~~~~~~~~k~vlVlGaG---g~a~ai~~aL~~~g~~~V~v~~R 155 (278)
T PRK00258 115 ERLGVDLKGKRILILGAG---GAARAVILPLLDLGVAEITIVNR 155 (278)
T ss_pred hccCCCCCCCEEEEEcCc---HHHHHHHHHHHHcCCCEEEEEeC
Confidence 2 2234667788888872 56666666666 35444555544
No 131
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=28.42 E-value=1.7e+02 Score=25.78 Aligned_cols=74 Identities=9% Similarity=0.080 Sum_probs=48.1
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEE--EeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHh
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVEL--KTRADTPDISNLQKCADFVHAFMLGFDVIDAIAL 119 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I--~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~L 119 (219)
..|.|=-.|-+.++|+.|..++.|.+.+.-.+.+ ....|.| ... ...+..+..-|..+..++.++.++-.|++-
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~--~~~~i~i~v~ev-~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ 121 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRFGF--PEGKVELFAERV-ENRGLCAMAQAESLRYKLLEGLPVRRAAYG 121 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHhCC--CCceEEEEEEEe-cCCCcCHHHHHHHHHHHHHhcCcHHHHHHH
Confidence 4455556677899999997777666554332211 1222322 221 124567888999999999999999888843
No 132
>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=27.62 E-value=1.5e+02 Score=30.05 Aligned_cols=91 Identities=21% Similarity=0.239 Sum_probs=53.6
Q ss_pred EEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHH---------c-----CCChHHHHHhhhc---CcceeeeEEecccccc
Q 027782 76 MNLKARRVELKTRADTPDISNLQKCADFVHAFM---------L-----GFDVIDAIALLRL---DELYVESFEIKDVKTL 138 (219)
Q Consensus 76 id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~---------r-----GF~~e~A~~Ll~~---Dd~~~e~i~I~dv~~~ 138 (219)
++.+.=.+.|-+ .||..+.+--|+|+.++ | =.++++|.++... ++.-+..+.-.+.
T Consensus 21 ~~~egp~~~~~~----~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~f~~~--- 93 (630)
T TIGR03675 21 VEFEGPELVIYT----KNPELFAKDDDLVKELAKKLRKRIVIRPDPSVLLPPEEAIEKIKEIVPEEAGITDIYFDDV--- 93 (630)
T ss_pred EEEeCCeEEEEe----CCHHHhccchHHHHHHHHHhhceEEEecChhhcCCHHHHHHHHHHhCCCcCCceeEEecCC---
Confidence 333444555554 67777766667777666 2 1456777766540 1111111111111
Q ss_pred cchhh--hhhhcceecCCCchHHHHHHhhCceEEEcC
Q 027782 139 RGEHL--SRAIGRLSGKGGKTKFAIENATKTRIVIAD 173 (219)
Q Consensus 139 ~~~~~--~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~ 173 (219)
+++.+ .+.-|.+||++|.|.+.|-..||-.-.|.-
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~ 130 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVR 130 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEe
Confidence 12222 234699999999999999999999888754
No 133
>COG0169 AroE Shikimate 5-dehydrogenase [Amino acid transport and metabolism]
Probab=27.45 E-value=1.1e+02 Score=27.89 Aligned_cols=113 Identities=22% Similarity=0.240 Sum_probs=72.6
Q ss_pred HHHHHHHHHHHHHHH-cCCCh-----HHHHHhhhcCcceeeeEEecccccc--cchhhhhh-hcceecCCCchHHHHHHh
Q 027782 94 ISNLQKCADFVHAFM-LGFDV-----IDAIALLRLDELYVESFEIKDVKTL--RGEHLSRA-IGRLSGKGGKTKFAIENA 164 (219)
Q Consensus 94 p~~i~KA~d~I~Ai~-rGF~~-----e~A~~Ll~~Dd~~~e~i~I~dv~~~--~~~~~~R~-~gRIIGk~G~t~~~IE~~ 164 (219)
|..+-.+-.-+++.. +||++ |.|+.+++ + +.+-... .-|-+.+. -|++.|-|=.-+=....+
T Consensus 45 ~~~l~~~v~~~~~~g~~G~NVTiP~Ke~~~~~lD--~-------l~~~A~~iGAVNTl~~~~~g~l~G~NTD~~G~~~~L 115 (283)
T COG0169 45 PEDLPEAVSGIRALGFRGLNVTIPFKEAALPLLD--E-------LSPRARLIGAVNTLVREDDGKLRGYNTDGIGFLRAL 115 (283)
T ss_pred HHHHHHHHHHHHhcCCCeeEECCccHHHHHHHHh--c-------CCHHHHHhCCceEEEEccCCEEEEEcCCHHHHHHHH
Confidence 566666666666554 55543 77778775 2 2222211 22455566 499999887777777777
Q ss_pred hCceE--EEcCceEEEeeCCchHHHHHHHHHHHHc-CCCChhhhHHHHHHHHHHhhc
Q 027782 165 TKTRI--VIADTKIHILGSFANIKIARDSLCSLIL-GSPAGKVYSKLRAVTARLAER 218 (219)
Q Consensus 165 Tg~~I--~V~~~tV~IiG~~~~i~~Ar~aI~~Li~-g~~~~~VY~~l~~~~~~~~~~ 218 (219)
....+ .+.++++.|+|.= -.||-++.-|.. |...=+|+|.=...++++.++
T Consensus 116 ~~~~~~~~~~~~~vlilGAG---GAarAv~~aL~~~g~~~i~V~NRt~~ra~~La~~ 169 (283)
T COG0169 116 KEFGLPVDVTGKRVLILGAG---GAARAVAFALAEAGAKRITVVNRTRERAEELADL 169 (283)
T ss_pred HhcCCCcccCCCEEEEECCc---HHHHHHHHHHHHcCCCEEEEEeCCHHHHHHHHHH
Confidence 76553 4457889999865 367778888884 888888988833334444443
No 134
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=26.17 E-value=56 Score=23.40 Aligned_cols=38 Identities=11% Similarity=-0.024 Sum_probs=30.4
Q ss_pred eeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEE
Q 027782 40 VQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMN 77 (219)
Q Consensus 40 ~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id 77 (219)
.....+.|..+..+.|||+.|++...|+...+..++-.
T Consensus 23 ~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~ 60 (77)
T cd02414 23 GDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRN 60 (77)
T ss_pred CCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhc
Confidence 34466788888899999999999999998877666543
No 135
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=26.15 E-value=59 Score=32.02 Aligned_cols=48 Identities=6% Similarity=-0.130 Sum_probs=39.0
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhhcccEEEEEcCCceEEEE
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELK 86 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~ 86 (219)
..-.....|-.+-+|++||..|+-++.|+..+++.|+|.-.+-.+.|+
T Consensus 45 ~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ 92 (629)
T KOG0336|consen 45 GEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVT 92 (629)
T ss_pred CCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEE
Confidence 344556778899999999999999999999999999998654444444
No 136
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=25.74 E-value=73 Score=22.80 Aligned_cols=33 Identities=18% Similarity=0.034 Sum_probs=24.0
Q ss_pred EEeeCCCc-----cccchhcCccchhHHHhhc-ccEEEE
Q 027782 44 KVNVPPHR-----YSPLKKVWMDIYTPIFEQM-KIDIRM 76 (219)
Q Consensus 44 ~I~IP~~R-----v~~lig~wg~i~k~i~e~~-~~~i~i 76 (219)
++-|-.+. +|..+|.+|..++.|.+.+ |-+|++
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 44455555 8999999999999999998 555544
No 137
>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=25.18 E-value=1e+02 Score=21.53 Aligned_cols=32 Identities=19% Similarity=0.363 Sum_probs=26.6
Q ss_pred hhCceEEEcC--ceEEEeeCCchHHHHHHHHHHH
Q 027782 164 ATKTRIVIAD--TKIHILGSFANIKIARDSLCSL 195 (219)
Q Consensus 164 ~Tg~~I~V~~--~tV~IiG~~~~i~~Ar~aI~~L 195 (219)
..+..|+.+. +.+.+.|+.+.++.+++.|..|
T Consensus 43 ~~~~~i~~d~~tNsliv~g~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 43 SSSGRIVADERTNSLIVRGTPEDLEQIRELIKQL 76 (82)
T ss_dssp HTTTEEEEECTTTEEEEEEEHHHHHHHHHHHHHH
T ss_pred CCCeEEEEECCCCEEEEEeCHHHHHHHHHHHHHH
Confidence 4556888887 4588899999999999999876
No 138
>COG0345 ProC Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]
Probab=25.01 E-value=96 Score=28.01 Aligned_cols=62 Identities=18% Similarity=0.180 Sum_probs=41.2
Q ss_pred HHHHHHHH-HHcCCChHHHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhh
Q 027782 99 KCADFVHA-FMLGFDVIDAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 99 KA~d~I~A-i~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~T 165 (219)
-.+.+..| +..|++.++|.+|.. . .+.-. ..+...+++|+...+.++.=++|.|+..|+.+-
T Consensus 179 ~iEal~~agv~~Gl~~~~A~~l~~-~-t~~Ga---akll~e~~~~p~~Lr~~VtSPGGtTiagl~~le 241 (266)
T COG0345 179 FIEALADAGVRLGLPREEARELAA-Q-TVAGA---AKLLLESGEHPAELRDQVTSPGGTTIAGLRVLE 241 (266)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHH-H-HHHHH---HHHHHhcCCCHHHHHHhCcCCCchHHHHHHHHH
Confidence 34444443 348999999998865 1 11000 011112567889999999999999999998775
No 139
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=24.94 E-value=37 Score=23.96 Aligned_cols=65 Identities=8% Similarity=0.191 Sum_probs=40.6
Q ss_pred EEEeeCCCccccchhcCc--cchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCC
Q 027782 43 QKVNVPPHRYSPLKKVWM--DIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGF 111 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg--~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF 111 (219)
+++.++.+++.-+.|..- +....+.+++|+.+... ..+.+.+....-. ..+....|++..++|.+
T Consensus 2 ~~i~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~-~~~~~~v~vP~~R---~Di~~~~DliEEiaR~y 68 (70)
T PF03484_consen 2 KKITLSLDKINKLLGIDISPEEIIKILKRLGFKVEKI-DGDTLEVTVPSYR---FDIEHEEDLIEEIARIY 68 (70)
T ss_dssp EEEEEEHHHHHHHHTS---HHHHHHHHHHTT-EEEE--CTTEEEEEEETTS---TT-SSHHHHHHHHHHHH
T ss_pred eEEEecHHHHHHHhCCCCCHHHHHHHHHHCCCEEEEC-CCCEEEEEcCCCc---CCcCcccHHHHHHHHHh
Confidence 457778888888888532 23333556778887774 4566666653322 47888899999988753
No 140
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=24.91 E-value=73 Score=24.18 Aligned_cols=27 Identities=22% Similarity=0.185 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 94 ISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 94 p~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
+.+..|++.+.++| +|.++++|+..|+
T Consensus 9 ~~S~kK~~~v~~~I-rg~~v~~A~~~L~ 35 (105)
T cd00336 9 RISPKKARLVARLI-RGMSVDEALAQLE 35 (105)
T ss_pred ccCHHHHHHHHHHH-cCCcHHHHHHHHH
Confidence 45678888888855 9999999998876
No 141
>TIGR00507 aroE shikimate 5-dehydrogenase. This model finds proteins from prokaryotes and functionally equivalent domains from larger, multifunctional proteins of fungi and plants. Below the trusted cutoff of 180, but above the noise cutoff of 20, are the putative shikimate dehydrogenases of Thermotoga maritima and Mycobacterium tuberculosis, and uncharacterized paralogs of shikimate dehydrogenase from E. coli and H. influenzae. The related enzyme quinate 5-dehydrogenase scores below the noise cutoff. A neighbor-joining tree, constructed with quinate 5-dehydrogenases as the outgroup, shows the Clamydial homolog as clustering among the shikimate dehydrogenases, although the sequence is unusual in the degree of sequence divergence and the presence of an additional N-terminal domain.
Probab=24.66 E-value=1e+02 Score=27.07 Aligned_cols=100 Identities=18% Similarity=0.172 Sum_probs=51.5
Q ss_pred HHHHHHHHHHHHHHH-cCCCh-----HHHHHhhhcCcceeeeEEecccccc--cchhhhhhhcceecCCCchHHHHHHhh
Q 027782 94 ISNLQKCADFVHAFM-LGFDV-----IDAIALLRLDELYVESFEIKDVKTL--RGEHLSRAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 94 p~~i~KA~d~I~Ai~-rGF~~-----e~A~~Ll~~Dd~~~e~i~I~dv~~~--~~~~~~R~~gRIIGk~G~t~~~IE~~T 165 (219)
|..+..+-+.+++.. +||++ ++++.+++ . +.+.... .-|-+.+.-|+++|.+=...=.+..+.
T Consensus 39 ~~~l~~~~~~~~~~~~~G~nVT~P~K~~~~~~~d--~-------~~~~A~~~gavNti~~~~g~l~g~NTD~~G~~~~l~ 109 (270)
T TIGR00507 39 PDDLEDALSGFFALGFKGANVTSPFKEEAFQFLD--E-------IDERAKLAGAVNTLKLEDGKLVGYNTDGIGLVSDLE 109 (270)
T ss_pred HHHHHHHHHHHHhcCCCEEEECcCCHHHHHHHhh--h-------CCHHHHHhCCceEEEeeCCEEEEEcCCHHHHHHHHH
Confidence 345555555555543 67654 66777774 1 1111110 112333345778887655444444443
Q ss_pred CceEEEcCceEEEeeCCchHHHHHHHHHHHHc-CCCChhhhH
Q 027782 166 KTRIVIADTKIHILGSFANIKIARDSLCSLIL-GSPAGKVYS 206 (219)
Q Consensus 166 g~~I~V~~~tV~IiG~~~~i~~Ar~aI~~Li~-g~~~~~VY~ 206 (219)
.......++++.++|.- .+++-++..|.. |. +=+|++
T Consensus 110 ~~~~~~~~k~vliiGaG---g~g~aia~~L~~~g~-~v~v~~ 147 (270)
T TIGR00507 110 RLIPLRPNQRVLIIGAG---GAARAVALPLLKADC-NVIIAN 147 (270)
T ss_pred hcCCCccCCEEEEEcCc---HHHHHHHHHHHHCCC-EEEEEe
Confidence 21222456778889873 566666666664 53 444543
No 142
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=24.03 E-value=78 Score=24.33 Aligned_cols=26 Identities=23% Similarity=0.236 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 95 SNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 95 ~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
.+..|++.+..+| ||.++++|+..|+
T Consensus 8 ~SpkK~~~va~~I-rG~~v~~A~~~L~ 33 (103)
T TIGR01044 8 ISPRKARLVADLI-RGKSVSQALDILR 33 (103)
T ss_pred cCHHHHHHHHHHH-cCCcHHHHHHHHh
Confidence 4668888888865 9999999998886
No 143
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=23.96 E-value=1.5e+02 Score=20.23 Aligned_cols=31 Identities=13% Similarity=0.108 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 91 TPDISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 91 t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
.-+...+.+.+.+..+...||+++++.++|+
T Consensus 38 ~yt~~di~~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 38 LFNDADIDRILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred ccCHHHHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 3567788888888888889999999988763
No 144
>PF11181 YflT: Heat induced stress protein YflT
Probab=23.56 E-value=63 Score=24.44 Aligned_cols=29 Identities=21% Similarity=0.391 Sum_probs=22.4
Q ss_pred EEeeCCchHHHHHHHHHHHHc-CCCChhhh
Q 027782 177 HILGSFANIKIARDSLCSLIL-GSPAGKVY 205 (219)
Q Consensus 177 ~IiG~~~~i~~Ar~aI~~Li~-g~~~~~VY 205 (219)
++||.|++.+.|..+|+.|-. |-....+|
T Consensus 1 ~~Igv~~~~~E~~~~I~~L~~~Gy~~ddI~ 30 (103)
T PF11181_consen 1 PVIGVYDNEEEALSAIEELKAQGYSEDDIY 30 (103)
T ss_pred CEEEEECCHHHHHHHHHHHHHcCCCcccEE
Confidence 478999999999999999984 66555444
No 145
>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=23.31 E-value=2.2e+02 Score=24.59 Aligned_cols=68 Identities=12% Similarity=0.139 Sum_probs=47.5
Q ss_pred EEEeeCCCccccchhcCccchhHHHhhccc-----EEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHH
Q 027782 43 QKVNVPPHRYSPLKKVWMDIYTPIFEQMKI-----DIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAI 117 (219)
Q Consensus 43 ~~I~IP~~Rv~~lig~wg~i~k~i~e~~~~-----~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~ 117 (219)
..|.|=-.|-+.++|+.|..++.|.+...- +++++. ++|.. .+..+..-|+.+...+.++.++-.|+
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~~~~~I~v----~ev~~----p~l~A~lvA~~Ia~qLe~rv~fRra~ 111 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGLENPQIDV----EEVEN----PELNAQVQAERIARSLERGLHFRRAA 111 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHHHhCCCceEEEE----EEEeC----CCcCHHHHHHHHHHHHHccccHHHHH
Confidence 445565667789999999877766544332 333332 34443 34567789999999999999999888
Q ss_pred H
Q 027782 118 A 118 (219)
Q Consensus 118 ~ 118 (219)
+
T Consensus 112 k 112 (195)
T TIGR01008 112 Y 112 (195)
T ss_pred H
Confidence 4
No 146
>PRK11901 hypothetical protein; Reviewed
Probab=22.86 E-value=84 Score=29.43 Aligned_cols=22 Identities=18% Similarity=0.353 Sum_probs=19.6
Q ss_pred eEEEeeCCchHHHHHHHHHHHH
Q 027782 175 KIHILGSFANIKIARDSLCSLI 196 (219)
Q Consensus 175 tV~IiG~~~~i~~Ar~aI~~Li 196 (219)
.|.+.|.|...+.|+.||..|=
T Consensus 284 YVVvyG~Y~Sr~eAk~Ai~sLP 305 (327)
T PRK11901 284 YVLVSGNYASSAEAKRAIATLP 305 (327)
T ss_pred EEEEecCcCCHHHHHHHHHhCC
Confidence 3888999999999999998873
No 147
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=22.03 E-value=1.4e+02 Score=26.48 Aligned_cols=65 Identities=14% Similarity=0.110 Sum_probs=52.1
Q ss_pred CccccchhcCccchhHHHhhcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 50 HRYSPLKKVWMDIYTPIFEQMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 50 ~Rv~~lig~wg~i~k~i~e~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
..+|-|.|+.|+++-.|++.++++|-+. ..+|.|-+ .-..+.-|++.|-.+..|-+|..-..-|+
T Consensus 178 RAIGRiaGk~GkTkfaIEn~trtrIVla--d~kIHiLG-----~~~niriAR~avcsLIlGsppgkVy~~LR 242 (252)
T KOG3273|consen 178 RAIGRIAGKGGKTKFAIENVTRTRIVLA--DSKIHILG-----AFQNIRIARDAVCSLILGSPPGKVYGNLR 242 (252)
T ss_pred HHHHHhhcCCCcceeeeeccceeEEEec--CceEEEee-----cchhhHHHHHhhHhhhccCCchhHHHHHH
Confidence 4578899999999999999998888764 56788875 45678899998888888988876665444
No 148
>TIGR02517 type_II_gspD general secretion pathway protein D. In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion, also called the main terminal branch of the general secretion pathway. Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See PubMed:12654803). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (TIGR02515) and to the type III secretion system pore YscC/HrcC (TIGR02516).
Probab=22.00 E-value=4.2e+02 Score=26.05 Aligned_cols=118 Identities=9% Similarity=0.156 Sum_probs=0.0
Q ss_pred CccchhHHHhhcccEEEEEcC-CceEEEEeCCCCCCHHHHHHHHHHHHHHHcCCCh-----HHHHHhhhc----------
Q 027782 59 WMDIYTPIFEQMKIDIRMNLK-ARRVELKTRADTPDISNLQKCADFVHAFMLGFDV-----IDAIALLRL---------- 122 (219)
Q Consensus 59 wg~i~k~i~e~~~~~i~id~~-~~~V~I~~~~~t~dp~~i~KA~d~I~Ai~rGF~~-----e~A~~Ll~~---------- 122 (219)
|.++.+.+.+.+|..+-+|.. .|+|.++. .++.....|-++++.+.+-... .+.+.+...
T Consensus 8 l~~vl~~~~~~~g~n~vid~~v~g~vtl~~----~~~v~~~eal~~l~~lL~~~gl~~~~~g~~~~I~~~~~~~~~~~~~ 83 (594)
T TIGR02517 8 ISTVVKAISDLTGKNFIIDPRVKGKITIIS----PRPVTEDEAYQLFLSALRAQGFAVVPEGNGYKIVVPRAAAKLSPGP 83 (594)
T ss_pred HHHHHHHHHHHhCCeEEECCCCceEEEEEe----CCCCCHHHHHHHHHHHHHhCCeEEEEeCCcEEEeCchHhcccCCCc
Q ss_pred -----------CcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhhCceEEEcC--ceEEEeeCCchHHHHH
Q 027782 123 -----------DELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENATKTRIVIAD--TKIHILGSFANIKIAR 189 (219)
Q Consensus 123 -----------Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~Tg~~I~V~~--~tV~IiG~~~~i~~Ar 189 (219)
.++...+|.+..+ +...+......+..++| .+.+++ +.+.+.|..++++.++
T Consensus 84 ~~~~~~~~~~~~~~~~~vi~L~~~---~a~~v~~~L~~lls~~~------------~v~~d~~~N~liv~~~~~~l~~i~ 148 (594)
T TIGR02517 84 IEDGPAPGVGGDQFVTRVFPLRNI---SASELVPVLRPLVSPNG------------DVAAYPPTNTIVVTDYASNINRVA 148 (594)
T ss_pred cccCCCCCCCCCceEEEEEEeccC---CHHHHHHHHHHhcCCCc------------eEEEcCCCCEEEEEcCHHHHHHHH
Q ss_pred HHHHHH
Q 027782 190 DSLCSL 195 (219)
Q Consensus 190 ~aI~~L 195 (219)
+.|..|
T Consensus 149 ~li~~l 154 (594)
T TIGR02517 149 RIIQQL 154 (594)
T ss_pred HHHHHh
No 149
>CHL00034 rpl22 ribosomal protein L22
Probab=21.89 E-value=84 Score=24.83 Aligned_cols=27 Identities=15% Similarity=0.207 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHcCCChHHHHHhhh
Q 027782 94 ISNLQKCADFVHAFMLGFDVIDAIALLR 121 (219)
Q Consensus 94 p~~i~KA~d~I~Ai~rGF~~e~A~~Ll~ 121 (219)
..+..|++.+..+| ||.++++|+..|+
T Consensus 18 r~SpkK~r~va~~I-RG~~v~~A~~~L~ 44 (117)
T CHL00034 18 RMSAHKARRVIDQI-RGRSYEEALMILE 44 (117)
T ss_pred ccCHHHHHHHHHHH-cCCcHHHHHHHHH
Confidence 45778888888865 9999999998876
No 150
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=21.64 E-value=2.6e+02 Score=19.39 Aligned_cols=34 Identities=6% Similarity=0.161 Sum_probs=29.7
Q ss_pred hcccEEEEEcCCceEEEEeCCCCCCHHHHHHHHHHHHHH
Q 027782 69 QMKIDIRMNLKARRVELKTRADTPDISNLQKCADFVHAF 107 (219)
Q Consensus 69 ~~~~~i~id~~~~~V~I~~~~~t~dp~~i~KA~d~I~Ai 107 (219)
..+.+|..|..++.+.|.. +|..+.+.+++|+.+
T Consensus 43 ~~~~~i~~d~~tNsliv~g-----~~~~~~~i~~li~~L 76 (82)
T PF03958_consen 43 SSSGRIVADERTNSLIVRG-----TPEDLEQIRELIKQL 76 (82)
T ss_dssp HTTTEEEEECTTTEEEEEE-----EHHHHHHHHHHHHHH
T ss_pred CCCeEEEEECCCCEEEEEe-----CHHHHHHHHHHHHHH
Confidence 3477999999999999995 789999999999876
No 151
>PRK14361 Maf-like protein; Provisional
Probab=20.96 E-value=1.3e+02 Score=25.60 Aligned_cols=26 Identities=27% Similarity=0.232 Sum_probs=21.3
Q ss_pred EeeCCchHHHHHHHHHHHHcCCCChhhh
Q 027782 178 ILGSFANIKIARDSLCSLILGSPAGKVY 205 (219)
Q Consensus 178 IiG~~~~i~~Ar~aI~~Li~g~~~~~VY 205 (219)
|+|.+.+.+.|++.+..| .|+.|. ||
T Consensus 74 ilgKP~~~eeA~~~L~~l-sG~~h~-V~ 99 (187)
T PRK14361 74 LLAKPADEAENEAFLRVL-SGRTHQ-VY 99 (187)
T ss_pred EecCCCCHHHHHHHHHHh-CCCceE-EE
Confidence 689999999999988777 788885 55
No 152
>PRK00468 hypothetical protein; Provisional
Probab=20.67 E-value=1e+02 Score=22.59 Aligned_cols=31 Identities=13% Similarity=0.056 Sum_probs=26.5
Q ss_pred ceeEEEEeeCCCccccchhcCccchhHHHhh
Q 027782 39 RVQFQKVNVPPHRYSPLKKVWMDIYTPIFEQ 69 (219)
Q Consensus 39 ~~~~~~I~IP~~Rv~~lig~wg~i~k~i~e~ 69 (219)
+.....+.+.++=+|-+||+.|.+.+.|...
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 4566789999999999999999999987644
No 153
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=20.35 E-value=83 Score=24.15 Aligned_cols=23 Identities=17% Similarity=0.229 Sum_probs=20.5
Q ss_pred cCCCChhhhHHHHHHHHHHhhcC
Q 027782 197 LGSPAGKVYSKLRAVTARLAERF 219 (219)
Q Consensus 197 ~g~~~~~VY~~l~~~~~~~~~~~ 219 (219)
.|.+.++||+.+.+..++|++.+
T Consensus 139 lgis~~tv~~~~~ra~~~Lr~~l 161 (161)
T TIGR02985 139 LGISVKTVEYHISKALKELRKEL 161 (161)
T ss_pred HCCCHHHHHHHHHHHHHHHHhhC
Confidence 58899999999999999998864
No 154
>PLN02688 pyrroline-5-carboxylate reductase
Probab=20.04 E-value=47 Score=28.64 Aligned_cols=55 Identities=16% Similarity=0.233 Sum_probs=39.4
Q ss_pred HHHcCCChHHHHHhhhcCcceeeeEEecccccccchhhhhhhcceecCCCchHHHHHHhh
Q 027782 106 AFMLGFDVIDAIALLRLDELYVESFEIKDVKTLRGEHLSRAIGRLSGKGGKTKFAIENAT 165 (219)
Q Consensus 106 Ai~rGF~~e~A~~Ll~~Dd~~~e~i~I~dv~~~~~~~~~R~~gRIIGk~G~t~~~IE~~T 165 (219)
+...|+++++|.+++. .-. ..+..+ + ..++.++...+.++.=++|-|...++.+-
T Consensus 187 ~~~~Gl~~~~a~~~~~-~~~-~gs~~l--~-~~~~~~~~~l~~~v~spgG~t~~~l~~l~ 241 (266)
T PLN02688 187 GVAAGLPRDVALSLAA-QTV-LGAAKM--V-LETGKHPGQLKDMVTSPGGTTIAGVHELE 241 (266)
T ss_pred HHHcCCCHHHHHHHHH-HHH-HHHHHH--H-HhcCCCHHHHHHhCCCCchHHHHHHHHHH
Confidence 3448999999999986 321 111111 1 12467889999999999999999998874
Done!