Query 017090
Match_columns 377
No_of_seqs 324 out of 1412
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 05:31:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017090hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00108 unknown protein; Prov 100.0 2.2E-50 4.7E-55 378.2 22.7 224 90-372 33-256 (257)
2 KOG2814 Transcription coactiva 100.0 1.6E-49 3.5E-54 377.5 16.6 283 18-370 58-345 (345)
3 PF10469 AKAP7_NLS: AKAP7 2'5' 100.0 2.3E-44 4.9E-49 333.0 21.1 207 93-370 1-209 (209)
4 COG1514 LigT 2'-5' RNA ligase 99.9 2.8E-26 6.1E-31 207.5 15.5 179 151-372 2-180 (180)
5 TIGR02258 2_5_ligase 2'-5' RNA 99.9 2.2E-24 4.9E-29 194.2 19.9 148 198-370 32-179 (179)
6 PRK15124 2'-5' RNA ligase; Pro 99.9 2.2E-24 4.7E-29 194.7 18.4 142 198-372 35-176 (176)
7 PRK13679 hypothetical protein; 99.7 3.3E-16 7.1E-21 140.3 17.1 139 199-371 30-168 (168)
8 PHA02574 57B hypothetical prot 99.6 5.5E-16 1.2E-20 135.9 7.1 110 150-310 9-118 (149)
9 cd02393 PNPase_KH Polynucleoti 99.5 1.1E-13 2.3E-18 103.8 7.2 60 17-79 2-61 (61)
10 PF13563 2_5_RNA_ligase2: 2'-5 99.4 4.1E-12 8.9E-17 110.4 9.9 129 200-354 21-150 (153)
11 cd02394 vigilin_like_KH K homo 99.3 1.8E-12 4E-17 96.9 6.4 60 19-79 2-62 (62)
12 PF00013 KH_1: KH domain syndr 99.3 2.8E-12 6.1E-17 95.3 4.5 60 18-78 1-60 (60)
13 PF05213 Corona_NS2A: Coronavi 99.2 4.3E-10 9.4E-15 102.2 13.1 167 92-368 5-177 (248)
14 TIGR02696 pppGpp_PNP guanosine 99.2 5.8E-11 1.3E-15 126.3 7.8 81 17-100 578-668 (719)
15 cd00105 KH-I K homology RNA-bi 99.1 2.3E-10 5E-15 85.4 6.6 60 19-79 2-64 (64)
16 cd02395 SF1_like-KH Splicing f 99.0 5.2E-10 1.1E-14 95.0 6.9 59 26-84 15-95 (120)
17 cd02396 PCBP_like_KH K homolog 99.0 1.2E-09 2.5E-14 82.7 6.9 59 19-78 2-64 (65)
18 TIGR03591 polynuc_phos polyrib 99.0 1.1E-09 2.3E-14 117.9 7.6 81 17-100 551-639 (684)
19 COG1185 Pnp Polyribonucleotide 98.9 1.1E-09 2.3E-14 114.7 6.1 84 15-101 550-641 (692)
20 smart00322 KH K homology RNA-b 98.9 7.4E-09 1.6E-13 77.0 8.1 65 17-82 3-68 (69)
21 PRK13763 putative RNA-processi 98.9 3.3E-09 7.1E-14 96.3 7.0 65 17-83 3-70 (180)
22 PF02834 LigT_PEase: LigT like 98.9 1.6E-09 3.5E-14 86.1 3.6 59 199-264 29-87 (87)
23 TIGR03665 arCOG04150 arCOG0415 98.8 3.5E-09 7.6E-14 95.5 5.3 62 21-84 2-65 (172)
24 PF13014 KH_3: KH domain 98.8 3.9E-09 8.5E-14 73.3 4.3 39 27-65 1-43 (43)
25 PLN00207 polyribonucleotide nu 98.8 4.9E-09 1.1E-13 114.0 6.2 80 18-100 686-775 (891)
26 KOG1676 K-homology type RNA bi 98.7 3.3E-08 7.1E-13 101.8 7.1 103 18-121 231-346 (600)
27 PRK11824 polynucleotide phosph 98.6 4.8E-08 1E-12 105.4 5.2 81 17-100 554-642 (693)
28 KOG0119 Splicing factor 1/bran 98.4 6.2E-07 1.3E-11 90.6 6.3 70 18-87 139-233 (554)
29 TIGR03665 arCOG04150 arCOG0415 98.3 1.6E-06 3.5E-11 78.2 6.1 54 26-84 98-151 (172)
30 PRK13763 putative RNA-processi 98.2 1.8E-06 3.9E-11 78.4 6.3 53 27-84 105-157 (180)
31 PRK04163 exosome complex RNA-b 98.2 3.5E-06 7.6E-11 79.7 6.9 66 18-86 146-211 (235)
32 KOG1676 K-homology type RNA bi 98.1 4.8E-05 1E-09 78.9 13.1 106 15-121 137-258 (600)
33 KOG2193 IGF-II mRNA-binding pr 97.9 8.1E-06 1.8E-10 81.2 3.9 103 18-123 200-310 (584)
34 KOG2191 RNA-binding protein NO 97.9 0.00016 3.4E-09 70.3 11.8 105 17-122 39-161 (402)
35 KOG1067 Predicted RNA-binding 97.8 1.7E-05 3.6E-10 81.6 4.3 80 18-101 598-690 (760)
36 KOG2191 RNA-binding protein NO 97.7 7.8E-05 1.7E-09 72.4 6.9 66 18-84 133-204 (402)
37 COG1094 Predicted RNA-binding 97.7 9.3E-05 2E-09 67.3 6.6 66 17-84 8-77 (194)
38 COG5176 MSL5 Splicing factor ( 97.7 5.5E-05 1.2E-09 69.1 5.0 72 13-84 144-221 (269)
39 KOG2193 IGF-II mRNA-binding pr 97.4 0.00017 3.6E-09 72.1 4.7 64 21-85 284-353 (584)
40 KOG1588 RNA-binding protein Sa 97.4 0.00016 3.4E-09 68.5 4.2 68 18-87 93-187 (259)
41 KOG2190 PolyC-binding proteins 97.3 0.00053 1.1E-08 71.2 7.4 67 17-84 138-208 (485)
42 KOG2208 Vigilin [Lipid transpo 97.3 0.0005 1.1E-08 75.1 7.1 103 17-123 347-450 (753)
43 KOG2192 PolyC-binding hnRNP-K 97.2 0.00085 1.8E-08 63.6 7.2 68 16-84 314-384 (390)
44 KOG0336 ATP-dependent RNA heli 97.2 0.00027 5.9E-09 70.9 3.2 67 18-85 48-114 (629)
45 TIGR03319 YmdA_YtgF conserved 97.1 0.001 2.2E-08 69.9 7.4 65 18-84 205-270 (514)
46 PRK00106 hypothetical protein; 97.1 0.0013 2.9E-08 69.0 7.5 66 18-85 226-292 (535)
47 COG1094 Predicted RNA-binding 97.1 0.00099 2.2E-08 60.7 5.7 53 27-84 112-164 (194)
48 PRK12704 phosphodiesterase; Pr 97.0 0.0015 3.2E-08 68.7 7.2 67 18-86 211-278 (520)
49 KOG2113 Predicted RNA binding 97.0 0.00046 1E-08 66.6 2.8 64 17-81 26-89 (394)
50 PF09749 HVSL: Uncharacterised 96.6 0.017 3.7E-07 54.7 10.7 103 201-312 86-190 (239)
51 PF02834 LigT_PEase: LigT like 96.5 0.0024 5.1E-08 50.4 3.3 76 273-362 8-87 (87)
52 COG1097 RRP4 RNA-binding prote 96.5 0.0048 1E-07 58.0 5.7 64 19-85 148-211 (239)
53 cd02134 NusA_KH NusA_K homolog 96.5 0.0037 8E-08 46.6 3.9 36 17-52 25-60 (61)
54 PRK12705 hypothetical protein; 96.2 0.0062 1.4E-07 63.6 5.0 66 18-85 199-265 (508)
55 PF07823 CPDase: Cyclic phosph 96.0 0.087 1.9E-06 48.5 11.2 138 206-370 40-196 (196)
56 KOG2814 Transcription coactiva 95.6 0.0026 5.6E-08 62.1 -0.6 153 203-369 128-283 (345)
57 KOG2192 PolyC-binding hnRNP-K 95.5 0.037 8.1E-07 52.7 6.9 64 18-82 49-113 (390)
58 KOG2190 PolyC-binding proteins 95.2 0.029 6.3E-07 58.5 5.5 104 19-122 45-167 (485)
59 TIGR03223 Phn_opern_protn puta 93.2 1.4 3E-05 41.6 11.6 143 203-372 56-228 (228)
60 PRK02821 hypothetical protein; 92.6 0.13 2.8E-06 40.4 3.2 32 15-46 29-60 (77)
61 PRK00468 hypothetical protein; 92.5 0.14 3.1E-06 39.9 3.3 31 15-45 28-58 (75)
62 KOG2208 Vigilin [Lipid transpo 92.2 0.11 2.3E-06 57.3 3.1 38 17-54 709-746 (753)
63 COG1837 Predicted RNA-binding 92.1 0.16 3.4E-06 39.7 3.1 31 14-44 27-57 (76)
64 KOG3273 Predicted RNA-binding 92.0 0.1 2.3E-06 47.8 2.3 53 27-84 179-231 (252)
65 PF13083 KH_4: KH domain; PDB: 91.2 0.11 2.4E-06 39.8 1.5 35 14-48 26-60 (73)
66 PRK01064 hypothetical protein; 91.0 0.27 5.8E-06 38.7 3.4 33 14-46 27-59 (78)
67 cd02409 KH-II KH-II (K homolo 90.8 0.35 7.6E-06 35.5 3.9 34 17-50 25-58 (68)
68 COG1855 ATPase (PilT family) [ 90.8 0.18 3.8E-06 52.0 2.8 41 17-57 486-526 (604)
69 PF14611 SLS: Mitochondrial in 90.7 0.9 1.9E-05 41.9 7.3 66 18-86 27-92 (210)
70 PRK08406 transcription elongat 90.6 0.31 6.7E-06 42.6 3.8 41 13-53 95-135 (140)
71 KOG2279 Kinase anchor protein 90.6 0.17 3.6E-06 52.8 2.4 97 18-119 69-166 (608)
72 PF07650 KH_2: KH domain syndr 89.0 0.23 5E-06 38.4 1.7 40 11-51 20-59 (78)
73 PRK13764 ATPase; Provisional 88.7 0.32 6.9E-06 52.2 3.0 43 15-57 479-521 (602)
74 PRK08406 transcription elongat 87.5 0.7 1.5E-05 40.3 3.8 86 18-118 33-124 (140)
75 cd02414 jag_KH jag_K homology 87.0 0.58 1.3E-05 36.3 2.7 36 17-52 24-59 (77)
76 KOG2113 Predicted RNA binding 85.7 0.59 1.3E-05 45.7 2.6 65 18-82 116-181 (394)
77 KOG2874 rRNA processing protei 85.5 1.6 3.4E-05 42.2 5.3 48 28-80 160-207 (356)
78 PF13184 KH_5: NusA-like KH do 84.8 0.89 1.9E-05 34.8 2.7 26 28-53 19-45 (69)
79 PHA02977 hypothetical protein; 84.0 3.9 8.5E-05 35.8 6.6 94 206-313 71-174 (201)
80 COG0195 NusA Transcription elo 82.1 1.7 3.7E-05 39.9 3.9 42 11-52 69-111 (190)
81 TIGR01952 nusA_arch NusA famil 80.3 1.6 3.5E-05 38.1 3.0 38 16-53 99-136 (141)
82 TIGR01952 nusA_arch NusA famil 80.3 2.4 5.2E-05 37.1 4.0 36 18-53 34-69 (141)
83 PF10469 AKAP7_NLS: AKAP7 2'5' 79.7 0.36 7.8E-06 44.5 -1.4 25 150-174 1-25 (209)
84 cd02413 40S_S3_KH K homology R 79.2 1.3 2.9E-05 34.9 1.9 43 11-54 25-67 (81)
85 PRK06418 transcription elongat 76.5 3.2 7E-05 37.3 3.8 35 18-53 62-96 (166)
86 COG0195 NusA Transcription elo 76.3 2.8 6.2E-05 38.5 3.5 37 18-54 143-179 (190)
87 PRK12328 nusA transcription el 73.7 3.7 7.9E-05 41.6 3.8 42 16-57 307-348 (374)
88 KOG3102 Uncharacterized conser 71.1 14 0.00031 34.5 6.6 101 201-312 118-219 (269)
89 COG5166 Uncharacterized conser 71.1 3.1 6.7E-05 43.5 2.6 67 18-84 450-524 (657)
90 cd02412 30S_S3_KH K homology R 69.7 4.2 9.2E-05 33.7 2.7 33 18-50 62-94 (109)
91 PRK12327 nusA transcription el 67.6 5.9 0.00013 40.0 3.8 39 16-54 302-340 (362)
92 PLN00108 unknown protein; Prov 67.3 1.1 2.5E-05 42.9 -1.3 29 146-174 32-61 (257)
93 PRK09202 nusA transcription el 67.1 5.5 0.00012 41.7 3.5 38 17-54 302-339 (470)
94 cd02410 archeal_CPSF_KH The ar 65.0 6.2 0.00013 34.7 2.9 36 18-53 77-112 (145)
95 PF00352 TBP: Transcription fa 61.5 15 0.00033 28.9 4.4 36 46-84 48-84 (86)
96 PRK12329 nusA transcription el 61.5 9.7 0.00021 39.4 4.0 39 16-54 334-372 (449)
97 cd02411 archeal_30S_S3_KH K ho 60.2 9.5 0.00021 30.1 3.0 29 19-47 40-68 (85)
98 PRK12328 nusA transcription el 59.0 12 0.00025 38.1 4.0 45 9-53 229-279 (374)
99 PRK12327 nusA transcription el 57.7 13 0.00028 37.6 4.1 45 9-53 223-273 (362)
100 KOG2279 Kinase anchor protein 56.2 6 0.00013 41.6 1.5 67 17-84 140-209 (608)
101 TIGR01953 NusA transcription t 55.5 15 0.00031 36.9 4.0 45 9-53 221-271 (341)
102 PF09749 HVSL: Uncharacterised 54.6 12 0.00026 35.3 3.2 71 148-232 138-210 (239)
103 COG1702 PhoH Phosphate starvat 51.9 39 0.00084 33.9 6.3 53 24-81 22-74 (348)
104 PF07823 CPDase: Cyclic phosph 50.6 17 0.00037 33.3 3.4 42 262-311 4-46 (196)
105 COG0092 RpsC Ribosomal protein 50.4 13 0.00029 35.1 2.7 35 18-52 52-86 (233)
106 COG0799 Uncharacterized homolo 47.7 99 0.0022 26.1 7.2 61 219-294 6-66 (115)
107 PRK09202 nusA transcription el 46.3 23 0.0005 37.1 4.0 46 8-53 222-273 (470)
108 COG1847 Jag Predicted RNA-bind 45.9 17 0.00038 33.7 2.6 38 15-52 89-126 (208)
109 PF06299 DUF1045: Protein of u 43.2 84 0.0018 28.1 6.5 75 271-353 51-151 (160)
110 PRK11538 ribosome-associated p 42.7 1.3E+02 0.0029 24.8 7.2 60 220-294 7-66 (105)
111 PRK15494 era GTPase Era; Provi 40.0 19 0.00042 35.7 2.2 34 19-52 275-317 (339)
112 PRK00089 era GTPase Era; Revie 39.7 20 0.00043 34.4 2.2 34 19-52 228-270 (292)
113 KOG4369 RTK signaling protein 39.1 11 0.00025 43.1 0.5 68 17-85 1340-1411(2131)
114 PF08302 tRNA_lig_CPD: Fungal 39.1 1.4E+02 0.0031 28.6 7.9 106 202-336 113-227 (257)
115 TIGR00436 era GTP-binding prot 38.0 19 0.00041 34.3 1.7 30 18-47 222-252 (270)
116 COG1782 Predicted metal-depend 36.8 24 0.00052 37.2 2.3 35 18-52 100-134 (637)
117 PRK12329 nusA transcription el 36.6 41 0.00089 34.9 3.9 28 26-53 277-305 (449)
118 COG4604 CeuD ABC-type enteroch 36.5 33 0.00071 32.3 2.9 63 18-84 19-82 (252)
119 COG5255 Uncharacterized protei 36.4 60 0.0013 30.3 4.5 34 202-235 176-210 (239)
120 PRK09256 hypothetical protein; 35.8 40 0.00086 29.4 3.2 54 32-87 23-100 (138)
121 PF08975 2H-phosphodiest: Doma 34.8 42 0.00092 28.5 3.1 27 94-121 14-40 (118)
122 PRK04191 rps3p 30S ribosomal p 33.1 40 0.00087 31.3 3.0 32 19-50 42-73 (207)
123 TIGR00090 iojap_ybeB iojap-lik 33.0 2.2E+02 0.0047 23.1 7.0 46 241-294 16-61 (99)
124 COG1159 Era GTPase [General fu 32.7 26 0.00057 34.4 1.7 26 19-44 231-257 (298)
125 CHL00048 rps3 ribosomal protei 32.3 42 0.00091 31.4 3.0 32 18-49 67-98 (214)
126 COG3638 ABC-type phosphate/pho 32.1 81 0.0017 30.3 4.8 48 16-67 20-67 (258)
127 PRK10334 mechanosensitive chan 32.1 2.5E+02 0.0053 27.4 8.4 83 204-294 185-268 (286)
128 PF00472 RF-1: RF-1 domain; I 30.8 70 0.0015 26.6 3.8 47 33-85 23-73 (113)
129 PF14611 SLS: Mitochondrial in 30.8 1.5E+02 0.0033 27.0 6.4 47 35-83 114-164 (210)
130 KOG3429 Predicted peptidyl-tRN 30.7 56 0.0012 29.3 3.3 55 31-87 49-128 (172)
131 PF07485 DUF1529: Domain of Un 29.6 2.5E+02 0.0055 23.9 7.0 56 216-288 66-121 (123)
132 TIGR03675 arCOG00543 arCOG0054 29.2 43 0.00093 36.4 2.8 36 18-53 94-129 (630)
133 COG1908 FrhD Coenzyme F420-red 28.6 1.9E+02 0.0041 24.8 5.9 36 256-294 93-128 (132)
134 smart00411 BHL bacterial (prok 28.0 63 0.0014 25.2 2.9 35 216-254 17-51 (90)
135 TIGR01008 rpsC_E_A ribosomal p 27.7 58 0.0013 30.1 3.0 31 18-48 39-69 (195)
136 PLN00062 TATA-box-binding prot 27.2 1E+02 0.0022 28.0 4.5 30 58-87 146-176 (179)
137 PRK15245 type III effector pho 26.5 4.4E+02 0.0095 24.8 8.4 92 202-305 102-205 (241)
138 cd00591 HU_IHF Integration hos 26.5 78 0.0017 24.4 3.2 35 216-254 16-50 (87)
139 PTZ00084 40S ribosomal protein 26.0 1.8E+02 0.0038 27.4 5.9 34 19-52 46-79 (220)
140 KOG1423 Ras-like GTPase ERA [C 25.6 58 0.0013 32.5 2.7 30 18-47 329-359 (379)
141 COG0097 RplF Ribosomal protein 25.1 1.1E+02 0.0023 27.9 4.2 34 46-82 119-152 (178)
142 cd04517 TLF TBP-like factors ( 25.0 1.1E+02 0.0024 27.5 4.4 37 46-85 46-83 (174)
143 cd04516 TBP_eukaryotes eukaryo 24.9 1.4E+02 0.003 27.0 4.9 38 45-85 45-83 (174)
144 PRK00394 transcription factor; 24.1 1.2E+02 0.0026 27.5 4.4 27 58-84 147-174 (179)
145 PRK15031 5-carboxymethyl-2-hyd 23.7 1.9E+02 0.004 24.8 5.2 45 203-247 60-105 (126)
146 cd00652 TBP_TLF TATA box bindi 23.2 1.5E+02 0.0031 26.7 4.7 26 58-83 147-173 (174)
147 cd04517 TLF TBP-like factors ( 23.2 1.5E+02 0.0032 26.8 4.7 26 58-83 147-173 (174)
148 cd00652 TBP_TLF TATA box bindi 22.4 1.6E+02 0.0036 26.4 4.9 36 47-85 47-83 (174)
149 cd04516 TBP_eukaryotes eukaryo 22.3 1.2E+02 0.0027 27.3 4.1 27 58-84 146-173 (174)
150 PF13382 Adenine_deam_C: Adeni 21.2 2E+02 0.0044 25.9 5.2 45 57-101 64-108 (171)
151 PLN00062 TATA-box-binding prot 21.1 1.8E+02 0.004 26.3 4.9 38 45-85 45-83 (179)
152 PTZ00179 60S ribosomal protein 20.8 1.9E+02 0.0041 26.5 5.0 38 46-83 126-164 (189)
153 PRK00310 rpsC 30S ribosomal pr 20.7 2.4E+02 0.0052 26.7 5.8 36 11-47 57-92 (232)
154 PRK00394 transcription factor; 20.5 1.8E+02 0.0039 26.3 4.8 36 47-85 46-82 (179)
155 cd04518 TBP_archaea archaeal T 20.5 1.6E+02 0.0035 26.6 4.4 27 58-84 146-173 (174)
156 TIGR01009 rpsC_bact ribosomal 20.4 95 0.0021 28.9 3.0 29 19-47 64-92 (211)
No 1
>PLN00108 unknown protein; Provisional
Probab=100.00 E-value=2.2e-50 Score=378.16 Aligned_cols=224 Identities=56% Similarity=0.961 Sum_probs=199.1
Q ss_pred CCCceeEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccCCchhHhhhhccccceeEEEeecCCCccceec
Q 017090 90 SLDYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKV 169 (377)
Q Consensus 90 ~~~~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~fvav~~~~~~~~~~v~~ 169 (377)
++.||||||||++++|+|++++..||+.||+..+. .|.
T Consensus 33 ~~~~THFlavPL~~~p~i~~~~~~Fk~~Vl~~~~~------------------------~~~------------------ 70 (257)
T PLN00108 33 REVFTHFVSLPLAIYPDLKKNIEAFQNSVLGNNDK------------------------DPL------------------ 70 (257)
T ss_pred CCCCCeEEEEEcCCCHHHHHHHHHHHHHHHhcccc------------------------ccc------------------
Confidence 56799999999965899999999999999976310 000
Q ss_pred ccccccccccccccCCCCCCCCCCCCcccccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEcc
Q 017090 170 DRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKG 249 (377)
Q Consensus 170 ~~~~~~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~G 249 (377)
.. .+.++++||++++|++|.+|||||+||.|.+++++++|.++|++|...+.++++++|+.|+|+|
T Consensus 71 -------~f-------~~~l~~~gid~siF~~p~~LHLTLgmL~L~~~eev~kA~~~L~s~~~~i~~~l~~~pl~I~lkG 136 (257)
T PLN00108 71 -------KF-------QSTLAEMGIEKSIFVSPKTFHLTVVMLKLENNESVVKAQNILKSICSNVRQALKDRPVFIRLRG 136 (257)
T ss_pred -------cc-------cccccccCCCHHHcCCCCceEEEEEEEEcCCHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEEEe
Confidence 00 0134488999999999999999999999999999999999999999888899989999999999
Q ss_pred ccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHH
Q 017090 250 LDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDAR 329 (377)
Q Consensus 250 l~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~ 329 (377)
|++||+||++++||||+|++.++.++|+.+|+.|.+.|.++||...+ .+++++||+||||++|++.. .+++.+|||+
T Consensus 137 L~~Mnddps~~~VLYA~Ve~~~~~~rLq~~ad~i~~~F~~aGL~~~d-~~~~vKLH~TlmNt~~rk~k--~~k~~sFDA~ 213 (257)
T PLN00108 137 LDCMNGSLDKTRVLYAPVEEVGHEGRLLNACHVIIDAFENAGFAGKD-AKSRLKLHATLMNASYRKDK--SKKMDTFDAR 213 (257)
T ss_pred ehhcCCCcccceEEEEeccccCchhHHHHHHHHHHHHHHHcCCcccc-cCcceeeEeEEechhhhhcc--cCccccccHH
Confidence 99999999999999999998777789999999999999999999642 35799999999999997653 3467899999
Q ss_pred HHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 017090 330 DIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 372 (377)
Q Consensus 330 ~il~~~~~~~fG~~~v~~I~Ls~~~~~~~~g~Y~~l~si~L~~ 372 (377)
+||++|++++||++.|++||||++++.+.+|||+|+++++|++
T Consensus 214 ~Il~~f~d~~FG~~~i~~vhls~r~s~~~dGyY~~~~sl~~~~ 256 (257)
T PLN00108 214 EIHKEFENKDWGTYLIREAHISQRYKYDPNGYFHCCASLPFPH 256 (257)
T ss_pred HHHHhccCcccceEEecEEEEEeecccCCCCCEEEEEEeecCC
Confidence 9999999999999999999999999998899999999999986
No 2
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=100.00 E-value=1.6e-49 Score=377.48 Aligned_cols=283 Identities=39% Similarity=0.602 Sum_probs=257.6
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCC-CCCcEEEEeCCHHHHHHHHHHHHHHHHhhhcCCCCCceeE
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK-KEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHF 96 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~-~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~~~~~~~~f 96 (377)
+.++.|+++++++|||+.|+|.++||+||+|+|.+|+++ ..+.|+|+|.++.+|.+|.+||..++++.++ +.+.+||
T Consensus 58 ~~si~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 58 SSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKEEIKIIGISRNCVIQALERIAKLIDSDRK--SFPITHF 135 (345)
T ss_pred hhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCCcceEEEeehhHHHHHHHHHHHHHHHHhhhh--cCchhhh
Confidence 678999999999999999999999999999999999998 4789999999999999999999999999886 6889999
Q ss_pred EEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccCCchhHhhhhccccceeEEEeecCCCccceecccccccc
Q 017090 97 VSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRTSIPI 176 (377)
Q Consensus 97 v~~Pl~~~p~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~fvav~~~~~~~~~~v~~~~~~~~~ 176 (377)
+++|++ ..+++++|..|++-....
T Consensus 136 lal~ln-e~eVqe~f~~fke~~~~~------------------------------------------------------- 159 (345)
T KOG2814|consen 136 LALPLN-EHEVQEGFLAFKELKPFI------------------------------------------------------- 159 (345)
T ss_pred hhhhcc-hHHHHHHHHHHHhhhhhH-------------------------------------------------------
Confidence 999997 788999999998433211
Q ss_pred cccccccCCCCCCCCCCCCcccccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCC
Q 017090 177 VGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGS 256 (377)
Q Consensus 177 ~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~d 256 (377)
+ ++-+.|++.++|++|.++||||+|+.+++++++++|+++|+.+.+++..+.+..|+.+.++|+++|++|
T Consensus 160 -e---------sl~~~g~~~s~F~~p~~~HLTvgm~~L~~dd~vq~a~e~les~~~e~~~~~~~kp~~i~lkG~~~mndd 229 (345)
T KOG2814|consen 160 -E---------SLLDGGIDKSLFQGPGTFHLTVGMLKLLNDDDVQKALEILESTFQEIRIDVGEKPLFIDLKGLDKMNDD 229 (345)
T ss_pred -H---------HhhccchhhccccCCceeeEEEEEEEecChHHHHHHHHHHHHHHHHHHhccCCCceeeeccchhhhcCC
Confidence 0 123568999999999999999999999999999999999999988888888889999999999999999
Q ss_pred CCCceEEEEeeeccCChhHHHHHH-HHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCC---CccccccHHHHH
Q 017090 257 KDKARILYAPVEEIGDGDRLLHAC-QVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGT---RRVDYFDARDIF 332 (377)
Q Consensus 257 p~~~rVLya~v~~~~~~~~L~~l~-~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~---~~~~~fda~~il 332 (377)
|..++||||+|++.+....|+..+ +.|..+|...|+... +++++++|+|+||++|++.++.. ++...||+++++
T Consensus 230 P~~~kVLYAkv~~~~~e~~l~~~~~~~i~~~f~~~~li~k--~~~~~kLH~TvmNsryrk~~~~~g~~K~~~~Fdar~il 307 (345)
T KOG2814|consen 230 PSLTKVLYAKVEPDDYEKFLQHRCGERILERFVASGLIKK--ESSSLKLHCTVMNSRYRKNGGEPGLVKESESFDAREIL 307 (345)
T ss_pred HhHheeeeeeccCcchHHHHHHHHHHHHHHHHHHhcchhc--cccccEEEEEEehhhhhhcCCCcchhhHhhhccHHHHH
Confidence 999999999999977778899999 999999999999885 48899999999999998765422 567789999999
Q ss_pred HHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeC
Q 017090 333 KQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPF 370 (377)
Q Consensus 333 ~~~~~~~fG~~~v~~I~Ls~~~~~~~~g~Y~~l~si~L 370 (377)
+.|+++.||++...++|+|.+...+.+|||.+++++||
T Consensus 308 k~fg~f~fg~~~~~eih~~~~~~~d~ng~y~~~gsi~f 345 (345)
T KOG2814|consen 308 KAFGQFLFGELKLQEIHLSVRFAADQNGNYNECGSIPF 345 (345)
T ss_pred HHHhhHhHhhcccceeeeeeeeccccccchhhhcCCCC
Confidence 99999999999999999999999889999999999987
No 3
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=100.00 E-value=2.3e-44 Score=333.04 Aligned_cols=207 Identities=37% Similarity=0.627 Sum_probs=181.8
Q ss_pred ceeEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccCCchhHhhhhccccceeEEEeecCCCccceecccc
Q 017090 93 YSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDRT 172 (377)
Q Consensus 93 ~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~fvav~~~~~~~~~~v~~~~~ 172 (377)
||||||||++ +|.|++.+..||+.|+..
T Consensus 1 pthFl~ipl~-~~~i~~~~~~fq~~v~~~--------------------------------------------------- 28 (209)
T PF10469_consen 1 PTHFLCIPLN-SPEIQEKFKEFQNEVLSK--------------------------------------------------- 28 (209)
T ss_pred CCeEEEEECC-CHHHHHHHHHHHHHHHhh---------------------------------------------------
Confidence 6999999995 999999999999999843
Q ss_pred cccccccccccCCCCCCCCCCCCcccccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCC-CCeEEEEcccc
Q 017090 173 SIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDN-RPLFIRLKGLD 251 (377)
Q Consensus 173 ~~~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~-~p~~l~l~Gl~ 251 (377)
++|+++++|++|++|||||+||+|.+++++++|.++|+++.+.+.+.+.. +|+.++|+||+
T Consensus 29 ------------------~~~~~~~~~i~~~~lHlTL~vl~L~~~~~i~~a~~~L~~~~~~i~~~~~~~~~~~i~l~Gl~ 90 (209)
T PF10469_consen 29 ------------------DPGLDESAFIPPEKLHLTLGVLSLDTDEEIEKAKEALKSLKQEIKDQLQNPPPLKITLKGLG 90 (209)
T ss_pred ------------------cCCCCHHHcCCcccceEEEEEeeCCCHHHHHHHHHHHHHHHHHHhhhccCCCCceEEeeech
Confidence 23678889999999999999999999999999999999999888876654 99999999999
Q ss_pred CCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHH
Q 017090 252 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDI 331 (377)
Q Consensus 252 ~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~i 331 (377)
+|++||++++||||++.++++...|+++++.|.+.|.++||...++.+.+|+||+||||++++.... .+...+||++++
T Consensus 91 ~f~~d~~~~~VLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~~~~~~H~Tl~n~~~~~~~~-~~~~~~~d~~~~ 169 (209)
T PF10469_consen 91 YFNDDPSKARVLYAKVSEDSNSERLQELANKLRERFQEAGLLVTDDRRFSFKPHITLMNTSYRKKKK-RRQGNKFDASEL 169 (209)
T ss_pred hhCCCCCcceEEEEcccccchHHHHHHHHHHHHHHHHHcCCccccccCCCcceEEEEEecccccccc-ccccCccccHHH
Confidence 9999999999999999986667999999999999999999998542223489999999999852111 111267899999
Q ss_pred HHHhCCCccccEEecEEEEEeeecCCC-CCceeEeEEEeC
Q 017090 332 FKQFGSKEWGEYLIKEAHLSQRFVYDE-SGFYHCCASIPF 370 (377)
Q Consensus 332 l~~~~~~~fG~~~v~~I~Ls~~~~~~~-~g~Y~~l~si~L 370 (377)
+++|.+++||.+.|++|+||+|+..++ +|||.++++++|
T Consensus 170 ~~~~~~~~fG~~~v~~i~Lc~m~~~~~~dg~Y~~~~~i~l 209 (209)
T PF10469_consen 170 LEKYKDFDFGEQPVEEIQLCSMGSTKPSDGYYQCIASIPL 209 (209)
T ss_pred HHHcCCCccceEEECEEEEEeCCCCCCCCCeEEEEEEecC
Confidence 999999999999999999999987665 999999999987
No 4
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.8e-26 Score=207.51 Aligned_cols=179 Identities=19% Similarity=0.321 Sum_probs=149.6
Q ss_pred cceeEEEeecCCCccceecccccccccccccccCCCCCCCCCCCCcccccCCCcceEEeeccccCCHHHHHHHHHHHHHh
Q 017090 151 EHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSI 230 (377)
Q Consensus 151 ~~fvav~~~~~~~~~~v~~~~~~~~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i 230 (377)
.+|+||.+ .+++.+++..++..+. ..+ ...|++++++||||.|||+++++.++.+.++|.++
T Consensus 2 RlFiAl~~-p~~i~~~i~~~~~~~~---------------~~~--~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i 63 (180)
T COG1514 2 RLFIALDP-PAEIAERLARIRARLK---------------GAR--AIKWVEPENLHITLKFLGEVDEDKADELIEALARI 63 (180)
T ss_pred eeEEEecC-CHHHHHHHHHHHHhcC---------------ccc--ccccccccCceEEEEccCCcCchHHHHHHHHHHHh
Confidence 58999988 5666777777765441 111 34599999999999999999999999999999988
Q ss_pred HHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeee
Q 017090 231 SSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMN 310 (377)
Q Consensus 231 ~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r 310 (377)
.. +. ||.|+++|+|+|++ +..+||+|+++.+ .+.|.+|++.|...+..+|+..+ .++|.||+||+|
T Consensus 64 ~~------~~-~f~i~l~g~g~F~~-~~~~rvi~~~v~~---~~~L~~L~~~l~~~~~~~g~~~~---~r~F~PHvTl~r 129 (180)
T COG1514 64 AA------PE-PFPITLDGAGSFPN-PRRPRVIWVGVEE---TEELRALAEELERALARLGLRPE---ERPFVPHVTLAR 129 (180)
T ss_pred hc------CC-ceEEEEeeEcccCC-CCCCcEEEEcCCC---cHHHHHHHHHHHHHHHhcCCCCC---CCCcCCCEEEEe
Confidence 42 23 99999999999998 9999999999985 47899999999999999999986 689999999999
Q ss_pred ecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 017090 311 IRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 372 (377)
Q Consensus 311 ~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~v~~I~Ls~~~~~~~~g~Y~~l~si~L~~ 372 (377)
.+.. . ...+++..+.+..||++.|++++|.++..+..++.|+++.+++|.+
T Consensus 130 ~k~~-~----------~~~~~~~~~~~~~~~~~~vd~~~L~~S~l~~~gp~Y~~~~~~~L~~ 180 (180)
T COG1514 130 VKSK-D----------KLVEALGEFKNVEFGEMEVDRFSLYSSTLTPGGPIYETLKEFPLSG 180 (180)
T ss_pred eccc-c----------hhhhhhhhhccccccceEeeEEEEEEEeeCCCCCEEEEEEEEecCC
Confidence 8651 1 1247788899999999999999997766655689999999999974
No 5
>TIGR02258 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles.
Probab=99.93 E-value=2.2e-24 Score=194.19 Aligned_cols=148 Identities=20% Similarity=0.400 Sum_probs=127.1
Q ss_pred cccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHH
Q 017090 198 IFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLL 277 (377)
Q Consensus 198 ~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~ 277 (377)
.|++++++||||.|+|+.++++++.+.++|+++. .++|.+++.|+++|++ +.+++|||++++++ ..|.
T Consensus 32 r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~--------~~~f~l~l~~~~~F~~-~~~~~vl~l~~~~~---~~L~ 99 (179)
T TIGR02258 32 KWVPPENLHITLKFLGEVDEEQVEELEDALAKIA--------EPPFTLKLEGIGVFGN-PKRPRVLWAGVEQS---EELT 99 (179)
T ss_pred EECChHHCEEEEEEccCCCHHHHHHHHHHHHHhc--------CCCeEEEEeeeeeCCC-CCCCeEEEEeeCCC---HHHH
Confidence 4999999999999999999999999988888762 3679999999999987 77889999999853 5899
Q ss_pred HHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCC
Q 017090 278 HACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYD 357 (377)
Q Consensus 278 ~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~v~~I~Ls~~~~~~ 357 (377)
+|++.+.+.+...|+..+ .++|+|||||+|..... .+..++++.+....++.+.|++|+|+++....
T Consensus 100 ~L~~~l~~~~~~~g~~~~---~~~f~PHiTlar~~~~~----------~~~~~~~~~~~~~~~~~~~v~~i~L~~S~~~~ 166 (179)
T TIGR02258 100 QLHADLERELAKLGFSKE---ERPFTPHITLARKKSGK----------PGVPEFLQEFANEEFGSFHVDEFHLYSSTLTP 166 (179)
T ss_pred HHHHHHHHHHHHcCCCCC---CCCcCCCEEEEEecCCc----------HhHHHHHHHhCCCCCCceEeeEEEEEEeeccC
Confidence 999999999999999865 68899999999965321 12446788888888999999999998887766
Q ss_pred CCCceeEeEEEeC
Q 017090 358 ESGFYHCCASIPF 370 (377)
Q Consensus 358 ~~g~Y~~l~si~L 370 (377)
.++.|+++++++|
T Consensus 167 ~g~~Y~~l~~~~l 179 (179)
T TIGR02258 167 GGPIYEPLARFQL 179 (179)
T ss_pred CCCcceEEEEEcC
Confidence 6789999999987
No 6
>PRK15124 2'-5' RNA ligase; Provisional
Probab=99.93 E-value=2.2e-24 Score=194.71 Aligned_cols=142 Identities=13% Similarity=0.185 Sum_probs=117.2
Q ss_pred cccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHH
Q 017090 198 IFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLL 277 (377)
Q Consensus 198 ~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~ 277 (377)
.|+++++|||||.|||++++++++.+.++++++ ..+||.|+++|+|+|++ |||||+++++ +...|.
T Consensus 35 rwv~~~nlHiTL~FlG~v~~~~~~~l~~~l~~~--------~~~pF~l~l~~~g~Fp~----prvlwlg~~~--~~~~L~ 100 (176)
T PRK15124 35 RPVAAANLHLTLAFLGEVSAEKQQALSQLAGRI--------RQPGFTLTLDDAGQWPR----SRVVWLGMRQ--PPRGLL 100 (176)
T ss_pred ccccccccEEEEEecCCCCHHHHHHHHHHHHhc--------ccCCeEEEECcccCcCC----CCEEEEEcCC--CCHHHH
Confidence 499999999999999999999999888888776 35899999999999973 5999999974 247899
Q ss_pred HHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCC
Q 017090 278 HACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYD 357 (377)
Q Consensus 278 ~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~v~~I~Ls~~~~~~ 357 (377)
.|++.|.+.+..+|+..+ .++|+|||||+|..... .. .. . ..+.| .+.|++++|.++..+.
T Consensus 101 ~L~~~l~~~l~~~G~~~e---~r~f~PHiTLaR~~~~~------~~--~~------~-~~~~~-~~~v~~~~L~~S~l~~ 161 (176)
T PRK15124 101 QLANMLRSQAARSGCYQS---PQPFHPHITLLRDASRP------VA--IP------P-PGFNW-SFPVTEFTLYASSFAR 161 (176)
T ss_pred HHHHHHHHHHHHcCCCCC---CCCCCCCEeeccCCCCc------cc--cc------C-CCCCC-ceEcCEEEEEEEeccC
Confidence 999999999999999875 79999999999964211 00 00 0 12344 5889999998887766
Q ss_pred CCCceeEeEEEeCCC
Q 017090 358 ESGFYHCCASIPFPE 372 (377)
Q Consensus 358 ~~g~Y~~l~si~L~~ 372 (377)
.++.|+++++++|.+
T Consensus 162 ~g~~Y~~l~~~~L~~ 176 (176)
T PRK15124 162 GRTRYTPLQRWPLTQ 176 (176)
T ss_pred CCCEEEEEEEEeCCC
Confidence 789999999999863
No 7
>PRK13679 hypothetical protein; Provisional
Probab=99.71 E-value=3.3e-16 Score=140.32 Aligned_cols=139 Identities=16% Similarity=0.197 Sum_probs=105.1
Q ss_pred ccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHH
Q 017090 199 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 278 (377)
Q Consensus 199 ~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~ 278 (377)
|++| ||||.|+|.+++++++++.++|+++.. ...||.+++.|+++|++ + ++|||+++++ .+.|++
T Consensus 30 ~v~p---HITL~f~g~~~~~~~~~l~~~l~~~~~------~~~pf~l~l~~~~~F~~-~--~~vl~l~~~~---~~~L~~ 94 (168)
T PRK13679 30 LIPP---HITLKEPFEISDEQLDSIVEELRAIAS------ETKPFTLHVTKVSSFAP-T--NNVIYFKVEK---TEELEE 94 (168)
T ss_pred cCCC---ceEEecCCCCCHHHHHHHHHHHHHHHh------cCCCEEEEEeccccCCC-C--CCEEEEEccC---CHHHHH
Confidence 6666 999999999999999999999888742 34899999999999975 2 3899999985 368999
Q ss_pred HHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCC
Q 017090 279 ACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDE 358 (377)
Q Consensus 279 l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~~~~~fG~~~v~~I~Ls~~~~~~~ 358 (377)
|++.|...+. + ..+ .++|.|||||+|..... ..-++.+.++. .+..+ .+.|++|+|..+. .
T Consensus 95 L~~~l~~~~~--~-~~~---~~~f~PHiTlar~~~~~--------~~~~~~~~l~~-~~~~~-~~~v~~i~L~~~~---~ 155 (168)
T PRK13679 95 LHERLHSGDF--Y-GEA---EYAFVPHITIGQGLSDD--------EHEDVLGQLKM-ADVDH-EETIDRFHLLYQL---E 155 (168)
T ss_pred HHHHHHhccc--c-ccc---CCCCCCeEEeeCCCCcH--------HHHHHHHHHhc-CCcce-eEEECeEEEEEEC---C
Confidence 9999887543 1 222 57899999999764321 11123344433 55555 6889999998552 4
Q ss_pred CCceeEeEEEeCC
Q 017090 359 SGFYHCCASIPFP 371 (377)
Q Consensus 359 ~g~Y~~l~si~L~ 371 (377)
++.|..+.++.|+
T Consensus 156 ~~~w~~~~~~~~~ 168 (168)
T PRK13679 156 NGSWTVYETFRLG 168 (168)
T ss_pred CCeEEEEEEeeCC
Confidence 6899999999985
No 8
>PHA02574 57B hypothetical protein; Provisional
Probab=99.62 E-value=5.5e-16 Score=135.91 Aligned_cols=110 Identities=12% Similarity=0.048 Sum_probs=85.7
Q ss_pred ccceeEEEeecCCCccceecccccccccccccccCCCCCCCCCCCCcccccCCCcceEEeeccccCCHHHHHHHHHHHHH
Q 017090 150 QEHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKS 229 (377)
Q Consensus 150 ~~~fvav~~~~~~~~~~v~~~~~~~~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~ 229 (377)
..-|||+.+.. ...+++...|..+. ...||+++||||||.| ++++++.+..
T Consensus 9 ~RlF~Al~~~~-~~r~~L~~lq~~l~--------------------~~r~V~~enLHlTL~F----~~~~v~~l~~---- 59 (149)
T PHA02574 9 QGTYVAAKFSE-ATLDALERLQRTLR--------------------IPNPVPRDKLHSTIVY----SRVYVPFIPA---- 59 (149)
T ss_pred ceEEEEEcCCH-HHHHHHHHHHHhcc--------------------CCcccCHHHCEEEEec----CHHHhHHHhc----
Confidence 46799998865 66777777776431 1349999999999999 4555554421
Q ss_pred hHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEee
Q 017090 230 ISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLM 309 (377)
Q Consensus 230 i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~ 309 (377)
..++|.+++.|+|+|++ + ++||+|++++ .+.|..|++.+++.+.. .+ .++|+||+||+
T Consensus 60 ---------~~~~F~l~l~glG~F~~-~-~~rvlWlg~~----~~~L~~L~~~l~~~l~~----~~---~r~F~PHITLa 117 (149)
T PHA02574 60 ---------SGSTEVASSGHLEVWET-Q-DKNALVLVLE----SEYLQCRHKYARALGAT----HD---FDDYTPHITLS 117 (149)
T ss_pred ---------cCCCeEEEeccccccCC-C-CCCEEEEEeC----CHHHHHHHHHHHHHhhc----CC---CCCcCCcEEEe
Confidence 35899999999999963 2 2599999996 37899999999999887 22 46899999999
Q ss_pred e
Q 017090 310 N 310 (377)
Q Consensus 310 r 310 (377)
|
T Consensus 118 R 118 (149)
T PHA02574 118 Y 118 (149)
T ss_pred e
Confidence 9
No 9
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.48 E-value=1.1e-13 Score=103.83 Aligned_cols=60 Identities=28% Similarity=0.429 Sum_probs=55.9
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHH
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQ 79 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~ 79 (377)
.+.++.||++++|.|||+||+|+|+|+++|||+|+|++ +|.|.|+|+++++++.|+++|+
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~---~g~v~I~G~~~~~v~~A~~~I~ 61 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED---DGTVYIAASDKEAAEKAKKMIE 61 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC---CCEEEEEeCCHHHHHHHHHHhC
Confidence 35789999999999999999999999999999999997 6899999998999999999874
No 10
>PF13563 2_5_RNA_ligase2: 2'-5' RNA ligase superfamily; PDB: 1IUH_A.
Probab=99.35 E-value=4.1e-12 Score=110.41 Aligned_cols=129 Identities=16% Similarity=0.216 Sum_probs=78.9
Q ss_pred cCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHH
Q 017090 200 IKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHA 279 (377)
Q Consensus 200 v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l 279 (377)
.....+||||.+.+..++.. +.+.+.|..+.. ..++|.++|.|+++|++ +.+|||+.+.. ...|.+|
T Consensus 21 ~~~~~pHITL~~~~~~~~~~-~~~~~~l~~~~~------~~~~f~l~l~~~~~F~~---~~~vi~l~~~~---~~~L~~L 87 (153)
T PF13563_consen 21 YPRWPPHITLAFPFDIDDSL-DELVEALARLAA------GFPPFELRLDGFGSFPG---KGRVIFLNVEP---SPELEAL 87 (153)
T ss_dssp --GGG-EEEEEEEEE--GGG-HHHHHHHHHHHH------HS--EEEEEEEEEEESS---SSSSEEEEEEE----HHHHHH
T ss_pred CCCCCCEeEEEecCcccccH-HHHHHHHHHHHc------cCCCeEEEEccEEEcCC---CCCEEEEEcCC---CHHHHHH
Confidence 44566999999999987643 555566665532 24889999999999974 22599999965 4899999
Q ss_pred HHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHh-CCCccccEEecEEEEEeee
Q 017090 280 CQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQF-GSKEWGEYLIKEAHLSQRF 354 (377)
Q Consensus 280 ~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~-~~~~fG~~~v~~I~Ls~~~ 354 (377)
++.|.+.|...|...+. .++|+|||||++...... +..+++.+ ......++.|++|.|.+..
T Consensus 88 ~~~l~~~~~~~~~~~~~--~~~~~PHiTia~~~~~~~-----------~~~~~~~~~~~~~~~~~~v~~l~L~~~~ 150 (153)
T PF13563_consen 88 HRALREALRPFGFKQDS--YRPFRPHITIARRLSPKQ-----------AAEAIEKLQSEFPPISFTVDELALVRSD 150 (153)
T ss_dssp HHHHHHHHHHHHGGGGG--GS----EEEEEEESS----------------------------EEEEE-EEEEEEEE
T ss_pred HHHHHHHHHHcCCcccc--CCCcceEEEEeccCCcch-----------hHHHHHHHhCcCCCcEEEEeEEEEEEEC
Confidence 99999999999887751 389999999999754321 12344444 2233347899999997654
No 11
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.35 E-value=1.8e-12 Score=96.94 Aligned_cols=60 Identities=38% Similarity=0.605 Sum_probs=54.8
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEeCCHHHHHHHHHHHH
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQ 79 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~-~~~v~I~g~~~~~v~~A~~~I~ 79 (377)
.++.||+++++.|||++|+++++|+++|||+|+||+.++ ++.|+|+|+ .+++..|+++|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-KENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-HHHHHHHHHHhC
Confidence 679999999999999999999999999999999998543 688999998 789999999873
No 12
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.29 E-value=2.8e-12 Score=95.27 Aligned_cols=60 Identities=38% Similarity=0.576 Sum_probs=53.9
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHH
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKI 78 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I 78 (377)
+..+.||.+++++|||++|+++++|+++|||+|+||+.++...|+|+| +.+++++|+++|
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 468999999999999999999999999999999998753235899999 689999999987
No 13
>PF05213 Corona_NS2A: Coronavirus NS2A protein; InterPro: IPR007878 This entry is represented by Coronavirus non-structural protein 2A (32kDa); it is a family of uncharacterised viral proteins. Members have a phosphoesterase module (2H) [] and are predicted to be involved in RNA modification. The viral group of 2H phosphoesterases contains proteins from two unrelated virus types: the type C rotaviruses (VP3 protein, IPR011181 from INTERPRO) that are double stranded multipartite RNA viruses and the coronaviruses (NS2 protein, this group) that are positive strand RNA viruses. Given that these viruses have vertebrate hosts, it is likely that the 2H phosphoesterase domain was derived from the host by one of virus groups followed by rapid sequence divergence []. Subsequently, it may have been exchanged between the viral families. Although the direction of the exchange is not clear, it is possible that a double stranded replicative form of a subgenomic RNA transcript of the coronavirus NS2 was stabilised by a rotavirus and incorporated into its multiple double stranded RNA genome []. These proteins can be utilised as novel drug targets because of their predicted RNA modification role.
Probab=99.17 E-value=4.3e-10 Score=102.25 Aligned_cols=167 Identities=17% Similarity=0.300 Sum_probs=119.2
Q ss_pred CceeEEEeccccchhhhccHHHHHHHHhcccccccccccCCCCCccCCchhHhhhhccccceeEEEeecCCCccceeccc
Q 017090 92 DYSHFVSLPLAVHPELVDKLVNFQNTILGITDVCLDENVGSKSNEDASDSEEKEQQVDQEHKVAVELNIGDNSERVKVDR 171 (377)
Q Consensus 92 ~~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~fvav~~~~~~~~~~v~~~~ 171 (377)
.++||+++|+.+-....++|...|-.+++++=-| + .|
T Consensus 5 ~P~HFin~Pl~~f~~f~~~~~~LQ~~~~~eG~d~----------------k---------------------------~Q 41 (248)
T PF05213_consen 5 KPTHFINFPLVQFEGFMLNFKDLQFQLLEEGVDC----------------K---------------------------LQ 41 (248)
T ss_pred CCCceeeccchhhhhHHHHHHHHHHHHHHcCCCc----------------c---------------------------cc
Confidence 3899999999855889999999999998763100 0 00
Q ss_pred ccccccccccccCCCCCCCCCCCCcccccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEcccc
Q 017090 172 TSIPIVGYEAKASRPSTSSDLGIDKSIFIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLD 251 (377)
Q Consensus 172 ~~~~~~~~~~~~~r~~~~~~~gi~~~~~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~ 251 (377)
+ .=||||+||-+ +++++..+..+|+++.+.+. + ....+++..-.
T Consensus 42 -------------k------------------aPHlSl~mL~I-sd~~i~~V~~~iq~ViddM~-~---~~~~it~tnp~ 85 (248)
T PF05213_consen 42 -------------K------------------APHLSLGMLDI-SDEDIPDVETAIQKVIDDMV-W---FEGDITFTNPH 85 (248)
T ss_pred -------------c------------------cCeeEEEEEEc-ChhhhhhHHHHHHHHHHHhh-c---ccceEEecCce
Confidence 0 11999999976 68899999888888754321 1 22277777777
Q ss_pred CCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHH
Q 017090 252 LMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDI 331 (377)
Q Consensus 252 ~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~i 331 (377)
.++ +.+.+.|+ .+.+++..|...|.+.|+..+ ..|.|.||+||+......-+ .
T Consensus 86 MLg------~~yV~nV~------Gv~slh~ki~n~~~~kgit~g--QSRmwIPHiTia~~~~~av~-----I-------- 138 (248)
T PF05213_consen 86 MLG------RCYVANVK------GVLSLHDKIVNVFRKKGITFG--QSRMWIPHITIAQLNDAAVR-----I-------- 138 (248)
T ss_pred eec------cEEEEecc------cHHHHHHHHHHHHHHhCcCcC--cccccccceehhhhhchheE-----e--------
Confidence 774 56666776 378889999999999999997 48999999999987542111 0
Q ss_pred HHHhCCCccc-cEEe-----cEEEEEeeecCCCCCceeEeEEE
Q 017090 332 FKQFGSKEWG-EYLI-----KEAHLSQRFVYDESGFYHCCASI 368 (377)
Q Consensus 332 l~~~~~~~fG-~~~v-----~~I~Ls~~~~~~~~g~Y~~l~si 368 (377)
...+|+ +.++ .++.|-.++....+|+|..+.+.
T Consensus 139 ----~~~qFny~~~~n~~~~~rle~VKlGa~K~dgfYe~i~s~ 177 (248)
T PF05213_consen 139 ----KEKQFNYKITINPSSPARLEFVKLGAEKKDGFYESIVSH 177 (248)
T ss_pred ----ccceeeeEeeccCCChhcCeEEEcCCcccCceeeeehhh
Confidence 012233 3344 67777788876778999988763
No 14
>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=99.15 E-value=5.8e-11 Score=126.32 Aligned_cols=81 Identities=20% Similarity=0.312 Sum_probs=73.3
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHH--hhhc-------
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIA--EAVE------- 87 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~--~~~~------- 87 (377)
++.+++||+++||.|||+||+|||+|+++||++|+|.. +|.|.|.|.+.+++++|+++|+.++. ++..
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---~G~V~I~a~d~~~~~~A~~~I~~i~~~~~~~vG~i~~Gk 654 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---DGTVYIGAADGPSAEAARAMINAIANPTMPEVGERFLGT 654 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---CcEEEEEeCCHHHHHHHHHHHHHhhCcCcCCCCCEEEEE
Confidence 38899999999999999999999999999999999976 79999999999999999999999998 3322
Q ss_pred -CCCCCceeEEEec
Q 017090 88 -SPSLDYSHFVSLP 100 (377)
Q Consensus 88 -~~~~~~~~fv~~P 100 (377)
.++.+||.||.|.
T Consensus 655 V~~I~dfGaFVel~ 668 (719)
T TIGR02696 655 VVKTTAFGAFVSLL 668 (719)
T ss_pred EEEEECceEEEEec
Confidence 2477899999985
No 15
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.09 E-value=2.3e-10 Score=85.43 Aligned_cols=60 Identities=38% Similarity=0.500 Sum_probs=53.4
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCC---CCCcEEEEeCCHHHHHHHHHHHH
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK---KEDSIIIEGNSTDSVAKASEKIQ 79 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~---~~~~v~I~g~~~~~v~~A~~~I~ 79 (377)
..+.||..++++|||++|+++++|+++|||+|.|+..+ .+..|.|.|+ .+++..|...|+
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~-~~~v~~a~~~i~ 64 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGT-PEAVEKAKELIL 64 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcC-HHHHHHHHHHhC
Confidence 57899999999999999999999999999999998864 2577999997 689999998763
No 16
>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=99.03 E-value=5.2e-10 Score=94.95 Aligned_cols=59 Identities=29% Similarity=0.492 Sum_probs=53.4
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCC--------------------CCCcEEEEeCC--HHHHHHHHHHHHHHHH
Q 017090 26 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSK--------------------KEDSIIIEGNS--TDSVAKASEKIQAIIA 83 (377)
Q Consensus 26 ~~~~~iIG~~G~tik~ie~et~~~I~ip~~~--------------------~~~~v~I~g~~--~~~v~~A~~~I~~iv~ 83 (377)
.|+|.||||||+|+|+|+++|||+|.|...+ +.+.|.|+|.+ .+++++|+++|+.|+.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 6789999999999999999999999998763 13889999999 9999999999999887
Q ss_pred h
Q 017090 84 E 84 (377)
Q Consensus 84 ~ 84 (377)
.
T Consensus 95 ~ 95 (120)
T cd02395 95 P 95 (120)
T ss_pred c
Confidence 5
No 17
>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=98.99 E-value=1.2e-09 Score=82.73 Aligned_cols=59 Identities=37% Similarity=0.398 Sum_probs=52.6
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEeCCHHHHHHHHHHH
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKI 78 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~----~~~v~I~g~~~~~v~~A~~~I 78 (377)
..+.||.+.+|.|||++|+++++|+++|||+|.|++... +..|+|+|. .+++..|..+|
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 64 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGK-PSAVQKALLLI 64 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeC-HHHHHHHHHhh
Confidence 578999999999999999999999999999999987542 356899997 78999999887
No 18
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.96 E-value=1.1e-09 Score=117.89 Aligned_cols=81 Identities=21% Similarity=0.370 Sum_probs=73.0
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhhc--------C
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE--------S 88 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~--------~ 88 (377)
++.+++||+++|+.||||||+|||+|+++|||+|+|.. +|.|.|.+.+.+.+++|.++|+.++..+.. .
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d---dG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~ 627 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED---DGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVV 627 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---CeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEE
Confidence 38899999999999999999999999999999999975 799999999999999999999999877533 2
Q ss_pred CCCCceeEEEec
Q 017090 89 PSLDYSHFVSLP 100 (377)
Q Consensus 89 ~~~~~~~fv~~P 100 (377)
++..|+.||.|.
T Consensus 628 ~I~~~GafVei~ 639 (684)
T TIGR03591 628 RIMDFGAFVEIL 639 (684)
T ss_pred EEeCCEEEEEEC
Confidence 466799999984
No 19
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.93 E-value=1.1e-09 Score=114.69 Aligned_cols=84 Identities=29% Similarity=0.406 Sum_probs=76.4
Q ss_pred cceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhhc-------
Q 017090 15 SLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE------- 87 (377)
Q Consensus 15 ~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~------- 87 (377)
--++.+++|++++|+.+||+||++|++|.++||++|+|.. +|+|.|.+.+.+.+.+|+++|+.++.++..
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---dGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~iy~G~ 626 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---DGTVKIAASDGESAKKAKERIEAITREVEVGEVYEGT 626 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---CCcEEEEecchHHHHHHHHHHHHHHhhcccccEEEEE
Confidence 3458999999999999999999999999999999999984 799999999999999999999999999855
Q ss_pred -CCCCCceeEEEecc
Q 017090 88 -SPSLDYSHFVSLPL 101 (377)
Q Consensus 88 -~~~~~~~~fv~~Pl 101 (377)
.++.+|++||+|.-
T Consensus 627 V~ri~~fGaFv~l~~ 641 (692)
T COG1185 627 VVRIVDFGAFVELLP 641 (692)
T ss_pred EEEEeecceEEEecC
Confidence 25778999999875
No 20
>smart00322 KH K homology RNA-binding domain.
Probab=98.90 E-value=7.4e-09 Score=77.01 Aligned_cols=65 Identities=38% Similarity=0.556 Sum_probs=57.3
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCC-CCCcEEEEeCCHHHHHHHHHHHHHHH
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK-KEDSIIIEGNSTDSVAKASEKIQAII 82 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~-~~~~v~I~g~~~~~v~~A~~~I~~iv 82 (377)
....+.||..+++++||++|++++.|+++|||+|.++... ....|.|.|+ .+++..|...|...+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~-~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGP-PENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcC-HHHHHHHHHHHHHHh
Confidence 3578999999999999999999999999999999998754 2478999998 789999999998654
No 21
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.89 E-value=3.3e-09 Score=96.34 Aligned_cols=65 Identities=31% Similarity=0.442 Sum_probs=60.4
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEE---eCCHHHHHHHHHHHHHHHH
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIE---GNSTDSVAKASEKIQAIIA 83 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~---g~~~~~v~~A~~~I~~iv~ 83 (377)
.+.++.||+++++.|||+||+++|.|+++|||+|+|.. ++|.|.|+ +.+++++.+|++.|++++.
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~--~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~ 70 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS--ETGEVIIEPTDGEDPLAVLKARDIVKAIGR 70 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC--CCCeEEEEeCCCCCHHHHHHHHHHHHHHhc
Confidence 36789999999999999999999999999999999986 34899999 8899999999999999987
No 22
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=98.86 E-value=1.6e-09 Score=86.08 Aligned_cols=59 Identities=20% Similarity=0.432 Sum_probs=51.5
Q ss_pred ccCCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEE
Q 017090 199 FIKPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILY 264 (377)
Q Consensus 199 ~v~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLy 264 (377)
|+++.++||||+|+|.+++++++.+++.|..+.. ...||.+++.|+++|++ ..+++|+|
T Consensus 29 ~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~~------~~~~f~~~~~~~~~f~s-~~~~rvi~ 87 (87)
T PF02834_consen 29 WVRPFNPHITLAFLGEVPPDQLPELIEALANIAS------RFPPFTLTVDGFGLFPS-RLRPRVIW 87 (87)
T ss_dssp EGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHHC------CCB-EEEEEEEEEEEEE-EETCEEEE
T ss_pred ccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhhc------cCCCeEEEEeEEEEeCC-CCCCCCcC
Confidence 8999999999999999999999999999888742 35899999999999986 44889999
No 23
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.84 E-value=3.5e-09 Score=95.46 Aligned_cols=62 Identities=31% Similarity=0.413 Sum_probs=56.9
Q ss_pred EEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEE--EeCCHHHHHHHHHHHHHHHHh
Q 017090 21 MQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIII--EGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 21 i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I--~g~~~~~v~~A~~~I~~iv~~ 84 (377)
+.||++++|.|||+||+|+|+|+++|||+|+|.. ++|.|.| .+.+++++.+|++.|+++...
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~--~~g~V~I~~~t~d~~~i~kA~~~I~~i~~g 65 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS--ETGEVKIEEEDEDPLAVMKAREVVKAIGRG 65 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc--CCceEEEecCCCCHHHHHHHHHHHHHHHcC
Confidence 6899999999999999999999999999999986 3488999 677899999999999998873
No 24
>PF13014 KH_3: KH domain
Probab=98.83 E-value=3.9e-09 Score=73.31 Aligned_cols=39 Identities=38% Similarity=0.572 Sum_probs=33.9
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCC---CCC-CCcEEEEe
Q 017090 27 VIRFIKGKEGSTQKKFEKEMGVKIILPS---SKK-EDSIIIEG 65 (377)
Q Consensus 27 ~~~~iIG~~G~tik~ie~et~~~I~ip~---~~~-~~~v~I~g 65 (377)
++++|||++|++|++|+++|||+|+||+ .+. +..|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~~~~~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPPENEPGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECCccCCCCCceEEEEEC
Confidence 5899999999999999999999999998 222 56788887
No 25
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.81 E-value=4.9e-09 Score=114.01 Aligned_cols=80 Identities=21% Similarity=0.319 Sum_probs=72.0
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcE-EEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhhc---------
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVK-IILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE--------- 87 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~-I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~--------- 87 (377)
+.+++||+++|+.|||+||+|||.|+++||++ |+|.. +|.|.|.|.+.+++++|+++|+.+..++..
T Consensus 686 i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d---dg~V~I~a~d~~~i~~A~~~I~~l~~~~~vG~iy~~g~V 762 (891)
T PLN00207 686 IHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD---DGTVKITAKDLSSLEKSKAIISSLTMVPTVGDIYRNCEI 762 (891)
T ss_pred eEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC---CeeEEEEeCCHHHHHHHHHHHHHHhcCcCCCcEEECcEE
Confidence 88999999999999999999999999999999 99975 799999999999999999999999765422
Q ss_pred CCCCCceeEEEec
Q 017090 88 SPSLDYSHFVSLP 100 (377)
Q Consensus 88 ~~~~~~~~fv~~P 100 (377)
+++.+||.||.|.
T Consensus 763 ~~I~~FGaFVeL~ 775 (891)
T PLN00207 763 KSIAPYGAFVEIA 775 (891)
T ss_pred EEEeccEEEEEeC
Confidence 2467799999985
No 26
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.68 E-value=3.3e-08 Score=101.78 Aligned_cols=103 Identities=26% Similarity=0.319 Sum_probs=82.7
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEeCCHHHHHHHHHHHHHHHHhhhcCC----
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVESP---- 89 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~----~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~~---- 89 (377)
...|+||...+|.|||++|+|||+|+.|||+||+|-+.++ +..+.|.|+ ++.++.|.+.|..||.++....
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~-~d~ie~Aa~lI~eii~~~~~~~~~~~ 309 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGT-VDQIEHAAELINEIIAEAEAGAGGGM 309 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecC-HHHHHHHHHHHHHHHHHHhccCCCCc
Confidence 7899999999999999999999999999999999954433 578999997 7899999999999999876531
Q ss_pred -----CCCceeEEEeccccchhhhccHHHHHHHHhcc
Q 017090 90 -----SLDYSHFVSLPLAVHPELVDKLVNFQNTILGI 121 (377)
Q Consensus 90 -----~~~~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~ 121 (377)
..--.-+..+|-.----++++-.+-.+.|-++
T Consensus 310 ~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~q 346 (600)
T KOG1676|consen 310 GGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQ 346 (600)
T ss_pred CCCCccceeeEEEeccccccccccCCCccchhhhccc
Confidence 01014456688765566788888877777654
No 27
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.58 E-value=4.8e-08 Score=105.43 Aligned_cols=81 Identities=23% Similarity=0.400 Sum_probs=72.4
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhhc--------C
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE--------S 88 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~--------~ 88 (377)
.+..++||+++++.+||+||+|||.|+++||++|+|.. +|.|.|.+.+.+.+++|+++|+.++.+... .
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d---~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~ 630 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED---DGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVV 630 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---CceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEE
Confidence 36789999999999999999999999999999999854 799999999999999999999999987533 2
Q ss_pred CCCCceeEEEec
Q 017090 89 PSLDYSHFVSLP 100 (377)
Q Consensus 89 ~~~~~~~fv~~P 100 (377)
++.+|+.||.|.
T Consensus 631 ~I~~fGafVei~ 642 (693)
T PRK11824 631 RIVDFGAFVEIL 642 (693)
T ss_pred EEECCeEEEEEC
Confidence 466799999986
No 28
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=98.35 E-value=6.2e-07 Score=90.57 Aligned_cols=70 Identities=26% Similarity=0.406 Sum_probs=58.9
Q ss_pred EEEEEeCc------cccccccCCCchhHHHHHHHhCcEEEcCCCCC-------------------CCcEEEEeCCHHHHH
Q 017090 18 VLDMQVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-------------------EDSIIIEGNSTDSVA 72 (377)
Q Consensus 18 ~~~i~Vp~------~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~-------------------~~~v~I~g~~~~~v~ 72 (377)
.-.+.||. .|+|+|||+.|.|.|+||+|||+||.|-..+. .=.|.|++.+.+.|+
T Consensus 139 ~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~eki~ 218 (554)
T KOG0119|consen 139 HDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEKIK 218 (554)
T ss_pred ccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHHHH
Confidence 44666765 68999999999999999999999999976331 125899999999999
Q ss_pred HHHHHHHHHHHhhhc
Q 017090 73 KASEKIQAIIAEAVE 87 (377)
Q Consensus 73 ~A~~~I~~iv~~~~~ 87 (377)
+|+..|+.|+.+++.
T Consensus 219 ~Ai~vienli~~av~ 233 (554)
T KOG0119|consen 219 KAIAVIENLIQSAVS 233 (554)
T ss_pred HHHHHHHHHHHhhcc
Confidence 999999999988543
No 29
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=98.26 E-value=1.6e-06 Score=78.21 Aligned_cols=54 Identities=28% Similarity=0.372 Sum_probs=49.7
Q ss_pred cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 26 SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 26 ~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
...|.|||++|+|++.||+.|||+|.|+. ..|.|.| +.++++.|++.|+.|+..
T Consensus 98 ~~~griIG~~G~t~~~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 98 RIKGRIIGEGGKTRRIIEELTGVSISVYG----KTVGIIG-DPEQVQIAREAIEMLIEG 151 (172)
T ss_pred HHHhhhcCCCcHHHHHHHHHHCCeEEEcC----CEEEEEC-CHHHHHHHHHHHHHHHcC
Confidence 36999999999999999999999999984 6899999 589999999999999965
No 30
>PRK13763 putative RNA-processing protein; Provisional
Probab=98.25 E-value=1.8e-06 Score=78.44 Aligned_cols=53 Identities=28% Similarity=0.407 Sum_probs=48.5
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 27 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 27 ~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
.+|.|||++|+|+|.||+.|||+|.|+. ..|.|.| +.++++.|++.|+.|+..
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~----~~v~i~G-~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYG----KTVAIIG-DPEQVEIAREAIEMLIEG 157 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcC----CEEEEEe-CHHHHHHHHHHHHHHHcC
Confidence 6899999999999999999999999984 5699999 479999999999999954
No 31
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.18 E-value=3.5e-06 Score=79.70 Aligned_cols=66 Identities=26% Similarity=0.311 Sum_probs=60.2
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhh
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAV 86 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~ 86 (377)
-..+.||+.+++.+||++|.+++.|.++|+++|.|-. +|.|.|+|++.+.+..|.++|+.+-.++.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~---NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ---NGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC---CcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 4568999999999999999999999999999999964 79999999999999999999998876643
No 32
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=98.07 E-value=4.8e-05 Score=78.86 Aligned_cols=106 Identities=21% Similarity=0.283 Sum_probs=82.4
Q ss_pred cceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC-----CCcEEEEeCCHHHHHHHHHHHHHHHHhhhc--
Q 017090 15 SLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-----EDSIIIEGNSTDSVAKASEKIQAIIAEAVE-- 87 (377)
Q Consensus 15 ~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~-----~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~-- 87 (377)
+..+..|.||..+.|.|||+||+|||.|++.+||++.+-..+. .....|+|. ...|+.|+..+..|+.+-..
T Consensus 137 ~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGd-p~~ve~a~~lV~dil~e~~~~~ 215 (600)
T KOG1676|consen 137 VETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGD-PDKVEQAKQLVADILREEDDEV 215 (600)
T ss_pred cceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCC-HHHHHHHHHHHHHHHHhcccCC
Confidence 4458899999999999999999999999999999999876543 347889995 68999999999999985211
Q ss_pred --------CCCC-CceeEEEeccccchhhhccHHHHHHHHhcc
Q 017090 88 --------SPSL-DYSHFVSLPLAVHPELVDKLVNFQNTILGI 121 (377)
Q Consensus 88 --------~~~~-~~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~ 121 (377)
++.- ..+--|-+|-+.--.|+++-++.+++|-.+
T Consensus 216 ~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~e 258 (600)
T KOG1676|consen 216 PGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNE 258 (600)
T ss_pred CccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhc
Confidence 0000 014456677654577899999998888654
No 33
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.91 E-value=8.1e-06 Score=81.20 Aligned_cols=103 Identities=23% Similarity=0.251 Sum_probs=74.2
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEeCCHHHHHHHHHHHHHHHHhhhcCCCCCc
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDY 93 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~----~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~~~~~~ 93 (377)
.+.+-||..++|.||||.|+|||.|-..|.|+|+|-+..+ +..|+|-|. .|+..+|+.+|..|+..-.+ .-.+
T Consensus 200 PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~t-pEg~s~Ac~~ILeimqkEA~--~~k~ 276 (584)
T KOG2193|consen 200 PLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHST-PEGTSKACKMILEIMQKEAV--DDKV 276 (584)
T ss_pred ceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecC-ccchHHHHHHHHHHHHHhhh--ccch
Confidence 4678899999999999999999999999999999977554 457889886 68999999999998754222 1223
Q ss_pred eeEEEeccccchhhhc----cHHHHHHHHhcccc
Q 017090 94 SHFVSLPLAVHPELVD----KLVNFQNTILGITD 123 (377)
Q Consensus 94 ~~fv~~Pl~~~p~I~~----~~~~f~~~Il~~~~ 123 (377)
+.-+-|.+--|..++| +-++..+.|.++.+
T Consensus 277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~Tg 310 (584)
T KOG2193|consen 277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTG 310 (584)
T ss_pred hhhcchhhhhhcchhhhhhhhccccHHHHHhhcC
Confidence 4333333223555444 44566667766643
No 34
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.87 E-value=0.00016 Score=70.32 Aligned_cols=105 Identities=22% Similarity=0.228 Sum_probs=79.3
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEeCCHHHHHHHHHHHHHHHHhhhc---
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEAVE--- 87 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~------~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~--- 87 (377)
..+.|-||.--.|.||||||.||.+|++||||+|+.-+..+ +..|-|.|. -+.++...+.|..-+.+.-.
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt-~eai~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGT-VEALNAVHEFIADKIREKPQAVA 117 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEecc-HHHHHHHHHHHHHHHHHhHHhhc
Confidence 47889999999999999999999999999999999987654 456889996 57888888888776665311
Q ss_pred C--CC-CC------ceeEEEeccccchhhhccHHHHHHHHhccc
Q 017090 88 S--PS-LD------YSHFVSLPLAVHPELVDKLVNFQNTILGIT 122 (377)
Q Consensus 88 ~--~~-~~------~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~~ 122 (377)
+ .+ .+ ...-+.+|-+.-.-|+++-..+.++|+++.
T Consensus 118 k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqs 161 (402)
T KOG2191|consen 118 KPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQS 161 (402)
T ss_pred CCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhh
Confidence 0 00 11 123455676555778888888888888763
No 35
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=97.81 E-value=1.7e-05 Score=81.63 Aligned_cols=80 Identities=24% Similarity=0.230 Sum_probs=69.9
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhhc----------
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVE---------- 87 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~---------- 87 (377)
..+++|+++....+|||+|...|+|+.|||+.-.++ +|++.|.+++....++|++.|..|+.....
T Consensus 598 ~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD----e~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~~l~~g~vy~ 673 (760)
T KOG1067|consen 598 LETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD----EGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQDLEFGGVYT 673 (760)
T ss_pred eeEEeecchhhheeecCccceeeeEeeeccceeeec----CceEEEEecCHHHHHHHHHHHHHHhcCccccceEeeeEEE
Confidence 789999999999999999999999999999766665 699999999999999999999999865322
Q ss_pred ---CCCCCceeEEEecc
Q 017090 88 ---SPSLDYSHFVSLPL 101 (377)
Q Consensus 88 ---~~~~~~~~fv~~Pl 101 (377)
+.+.+++.||.|+-
T Consensus 674 ~tIt~~rd~G~~V~l~p 690 (760)
T KOG1067|consen 674 ATITEIRDTGVMVELYP 690 (760)
T ss_pred EEEeeecccceEEEecC
Confidence 23667999999875
No 36
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.71 E-value=7.8e-05 Score=72.35 Aligned_cols=66 Identities=27% Similarity=0.355 Sum_probs=55.4
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~------~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
.+.+-||..--|+||||||.|||.++++.+|-|+|-+... +..|++.|. .+...+|..+|..-+.+
T Consensus 133 qikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge-~e~~~~A~~~IL~Ki~e 204 (402)
T KOG2191|consen 133 QIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGE-PEQNMKAVSLILQKIQE 204 (402)
T ss_pred eeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCC-HHHHHHHHHHHHHHhhc
Confidence 5788899999999999999999999999999999964443 345777775 78999999998876654
No 37
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.69 E-value=9.3e-05 Score=67.35 Aligned_cols=66 Identities=27% Similarity=0.340 Sum_probs=59.8
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeC----CHHHHHHHHHHHHHHHHh
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIAE 84 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~----~~~~v~~A~~~I~~iv~~ 84 (377)
++..+.||++.++.+||+.|++.+.||+.|+|++.++. .+|.|.|+.. ++-.+.+|++.|++|...
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~--~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG 77 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS--KTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC--CCCeEEEEecCCCCChHHHHHHHHHHHHHhcC
Confidence 46679999999999999999999999999999999987 4689999886 889999999999999754
No 38
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=97.67 E-value=5.5e-05 Score=69.05 Aligned_cols=72 Identities=19% Similarity=0.240 Sum_probs=58.0
Q ss_pred cccceEEEEEeCc------cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 13 LISLSVLDMQVGA------SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 13 ~~~~~~~~i~Vp~------~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
|-....-.+.||. .|+|+||||.|.|+|+||+.|+|+|-|-..+...+..|.+..+++...|.+-|.-++..
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~p~~~~N~e~~lhcLI~a 221 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDTPESLKNAEAVLHCLIEA 221 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccCchhhhhhHHhHHHHhhc
Confidence 3344466778875 68999999999999999999999999987766556677777677888888888777654
No 39
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=97.41 E-value=0.00017 Score=72.08 Aligned_cols=64 Identities=27% Similarity=0.463 Sum_probs=53.2
Q ss_pred EEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEeCCHHHHHHHHHHHHHHHHhh
Q 017090 21 MQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGNSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 21 i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~------~~~v~I~g~~~~~v~~A~~~I~~iv~~~ 85 (377)
+.--..+.|.+||+.|+++|+||++|||+|.|.+--+ +.+|++.| +-|++.+|...|-.-+.++
T Consensus 284 ~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkG-siEac~~AE~eImkKlre~ 353 (584)
T KOG2193|consen 284 ILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKG-SIEACVQAEAEIMKKLREC 353 (584)
T ss_pred hhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecc-cHHHHHHHHHHHHHHHHHH
Confidence 3345689999999999999999999999999977543 57899999 6789999988887666554
No 40
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.40 E-value=0.00016 Score=68.55 Aligned_cols=68 Identities=22% Similarity=0.331 Sum_probs=49.7
Q ss_pred EEEEEeCcc------ccccccCCCchhHHHHHHHhCcEEEcCCCCC---------------------CCcEEEEeCCHHH
Q 017090 18 VLDMQVGAS------VIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---------------------EDSIIIEGNSTDS 70 (377)
Q Consensus 18 ~~~i~Vp~~------~~~~iIG~~G~tik~ie~et~~~I~ip~~~~---------------------~~~v~I~g~~~~~ 70 (377)
...|.||.. |+|.|+||+|.|+|+||++|||+|-|-.+++ .=.|.|+... -
T Consensus 93 ~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~--p 170 (259)
T KOG1588|consen 93 TEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA--P 170 (259)
T ss_pred EEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC--C
Confidence 677888875 9999999999999999999999999976553 0135565543 3
Q ss_pred HHHHHHHHHHHHHhhhc
Q 017090 71 VAKASEKIQAIIAEAVE 87 (377)
Q Consensus 71 v~~A~~~I~~iv~~~~~ 87 (377)
-..|..+|..-+++.++
T Consensus 171 ~~ea~~rl~~AleeI~k 187 (259)
T KOG1588|consen 171 PAEAYARLAYALEEIKK 187 (259)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45566666666666443
No 41
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=97.32 E-value=0.00053 Score=71.24 Aligned_cols=67 Identities=31% Similarity=0.401 Sum_probs=58.4
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCC----CCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSK----KEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~----~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
....+-||...+|-||||+|+.||+|.++||++|.|-+.. .+..|+|.|. .+.|.+|...|-.++.+
T Consensus 138 v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP~ster~V~IsG~-~~av~~al~~Is~~L~~ 208 (485)
T KOG2190|consen 138 VTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLPNSTERAVTISGE-PDAVKKALVQISSRLLE 208 (485)
T ss_pred eEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCCcccceeEEEcCc-hHHHHHHHHHHHHHHHh
Confidence 4678889999999999999999999999999999995531 2456999997 68999999999998877
No 42
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=97.28 E-value=0.0005 Score=75.11 Aligned_cols=103 Identities=27% Similarity=0.402 Sum_probs=89.2
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEeCCHHHHHHHHHHHHHHHHhhhcCCCCCcee
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSH 95 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~-~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~~~~~~~~ 95 (377)
....+.|-++++.+++|++|.++.+|+++++|.|++|..++ ...|+++|.+ .++.+|.+.++.++.+...+ ...+
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~~~~~~~v~~~~~~-~~~~ka~~~v~~~~~ei~n~---~~~~ 422 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQGSNNKKVVITGVS-ANDEKAVEDVEKIIAEILNS---IVKE 422 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccccCCCCCeEEeccc-cchhHHHHHHHHHHHhhhcc---cccc
Confidence 46788999999999999999999999999999999999655 5779999974 79999999999999885542 2466
Q ss_pred EEEeccccchhhhccHHHHHHHHhcccc
Q 017090 96 FVSLPLAVHPELVDKLVNFQNTILGITD 123 (377)
Q Consensus 96 fv~~Pl~~~p~I~~~~~~f~~~Il~~~~ 123 (377)
-+.+|-..|..|.+.-....+.|+.+..
T Consensus 423 ~~~iP~k~~~~iig~~g~~i~~I~~k~~ 450 (753)
T KOG2208|consen 423 EVQIPTKSHKRIIGTKGALINYIMGKHG 450 (753)
T ss_pred eeecCccchhhhhccccccHHHHHhhcC
Confidence 6778987899999999999999998843
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=97.25 E-value=0.00085 Score=63.59 Aligned_cols=68 Identities=21% Similarity=0.320 Sum_probs=56.3
Q ss_pred ceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC---CCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 16 LSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK---EDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~---~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
..+..+.||+++-|-|||+||..|++|..|.|+.|.|+.+-+ +..|+|+|+ .+.+..|-=..+.-|..
T Consensus 314 itTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGT-qdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 314 ITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGT-QDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred eeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEecc-HHHHhhHHHHHHHHHHh
Confidence 347789999999999999999999999999999999976432 456889997 57888887776666553
No 44
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.16 E-value=0.00027 Score=70.86 Aligned_cols=67 Identities=18% Similarity=0.226 Sum_probs=59.1
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhh
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~ 85 (377)
.+.+.|-+.++|.+||.||+.|++|+..|+|+|+|...+.+-.|+|.|. .+.-.+|..-|+..++..
T Consensus 48 plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~~e~kv~ifg~-~~m~~kaka~id~~~~k~ 114 (629)
T KOG0336|consen 48 PLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCDLEVKVTIFGI-NHMRKKAKASIDRGQDKD 114 (629)
T ss_pred chhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccCceeEEEEech-HHHHHHHHhhHhhhhhhh
Confidence 6788899999999999999999999999999999988666778999996 568888999898888654
No 45
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=97.14 E-value=0.001 Score=69.88 Aligned_cols=65 Identities=20% Similarity=0.330 Sum_probs=58.4
Q ss_pred EEEEEeCc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 18 VLDMQVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 18 ~~~i~Vp~-~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
+-.|.+|+ ++-|.|||+.|.+||.+|.-|||.|.|++ ..+.|+|+|-++-.-+-|+.-++.|+.+
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC--CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 66789999 77899999999999999999999999986 3568999998888889999999999877
No 46
>PRK00106 hypothetical protein; Provisional
Probab=97.08 E-value=0.0013 Score=68.98 Aligned_cols=66 Identities=15% Similarity=0.342 Sum_probs=58.5
Q ss_pred EEEEEeCc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhh
Q 017090 18 VLDMQVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 18 ~~~i~Vp~-~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~ 85 (377)
+-.|.+|. ++-|.|||+.|.+||.+|.-|||.|.|++ ..+.|+|+|-++-.-+-|+.-++.|+.+-
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd--tp~~v~lS~fdpvRReiAr~~le~Li~dg 292 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD--TPEVVVLSGFDPIRREIARMTLESLIKDG 292 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC--CCCeEEEeCCChHHHHHHHHHHHHHHHcC
Confidence 66789999 78899999999999999999999999986 35689999988888999999888888763
No 47
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.07 E-value=0.00099 Score=60.72 Aligned_cols=53 Identities=28% Similarity=0.409 Sum_probs=47.9
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 27 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 27 ~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
..|.|||++|+|.+.||+=|||.|.|- ..+|-|-|. .++++-|++.|+.++..
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~----g~tVaiiG~-~~~v~iAr~AVemli~G 164 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVY----GKTVAIIGG-FEQVEIAREAVEMLING 164 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEe----CcEEEEecC-hhhhHHHHHHHHHHHcC
Confidence 368999999999999999999999995 368999997 57999999999999976
No 48
>PRK12704 phosphodiesterase; Provisional
Probab=97.02 E-value=0.0015 Score=68.68 Aligned_cols=67 Identities=18% Similarity=0.300 Sum_probs=58.1
Q ss_pred EEEEEeCc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhh
Q 017090 18 VLDMQVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAV 86 (377)
Q Consensus 18 ~~~i~Vp~-~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~ 86 (377)
+-+|.+|. ++-|.|||+.|.+||.+|.-|||.|.|++ ..+.|+|+|.++-.-+.|+.-++.++.+.+
T Consensus 211 ~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd--tp~~v~ls~~~~~rre~a~~~l~~l~~dg~ 278 (520)
T PRK12704 211 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD--TPEAVILSGFDPIRREIARLALEKLVQDGR 278 (520)
T ss_pred eeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC--CCCeEEEecCChhhHHHHHHHHHHHHhcCC
Confidence 56788999 67899999999999999999999999986 356899999887777799999998887643
No 49
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=96.99 E-value=0.00046 Score=66.62 Aligned_cols=64 Identities=20% Similarity=0.294 Sum_probs=58.0
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHH
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 81 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~i 81 (377)
...+++||..+.+.|.|++|.+||.|..+|++.|.-|+++++-...++|- .+.|..|+..|.+.
T Consensus 26 vt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePiF~vTg~-~edv~~aRrei~sa 89 (394)
T KOG2113|consen 26 VTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPIFPVTGR-HEDVRRARREIPSA 89 (394)
T ss_pred cceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCCcceeccC-chhHHHHhhcCccc
Confidence 37889999999999999999999999999999999999988866778886 57999999999873
No 50
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=96.64 E-value=0.017 Score=54.67 Aligned_cols=103 Identities=18% Similarity=0.319 Sum_probs=77.8
Q ss_pred CCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEE-eeeccCChhHHHHH
Q 017090 201 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYA-PVEEIGDGDRLLHA 279 (377)
Q Consensus 201 ~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya-~v~~~~~~~~L~~l 279 (377)
.+.-|||+|.=---+...+++.-.+.|+.. +.. ....+|.+.+.++.+|.+ .++.|...+ .|... ....|..|
T Consensus 86 ~~~~lHISLSr~~~lr~~~id~f~~~lr~~---l~~-~~~~~F~v~f~~~~~~~N-~e~TR~FL~l~V~~~-~~~~l~~l 159 (239)
T PF09749_consen 86 SPDPLHISLSRTFPLRTHQIDPFVDSLRQA---LRS-SNIRPFYVSFSGLDVYTN-DEKTRSFLALRVSEG-SNNELKRL 159 (239)
T ss_pred CCCCeEEEeCCCccccHHHHHHHHHHHHHH---Hhh-cCCceEEEEeCceEEEec-CCCCeEEEEEEeccc-ccHHHHHH
Confidence 578899999866555668888777666654 211 245899999999999987 566675333 56542 22339999
Q ss_pred HHHHHHHHHHCCCcccccCC-CCeeeeEEeeeec
Q 017090 280 CQVIIDAFNEAGLVFHRDYN-KKLKLHATLMNIR 312 (377)
Q Consensus 280 ~~~l~~~f~~~Gl~~~~~~~-r~fkpHiTL~r~~ 312 (377)
.+.+.+.+.+.|+..- . ..-.+||.||-+-
T Consensus 160 ~~~i~~~l~~~~lp~~---Y~~~~~fHvSIAw~~ 190 (239)
T PF09749_consen 160 LDRINEVLKEFGLPPF---YDEDPSFHVSIAWTL 190 (239)
T ss_pred HHHHHHHHHHhCCCcc---cCCCCCCEEEEEEEC
Confidence 9999999999999874 5 7889999999875
No 51
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=96.51 E-value=0.0024 Score=50.40 Aligned_cols=76 Identities=9% Similarity=0.118 Sum_probs=50.9
Q ss_pred hhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHhCCC--ccc--cEEecEE
Q 017090 273 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK--EWG--EYLIKEA 348 (377)
Q Consensus 273 ~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~~~~--~fG--~~~v~~I 348 (377)
.+.|.++++.+.+.+...|+..+ +++.||+||++...... -.+.++.+..... .+. ++.++++
T Consensus 8 ~~~L~~l~~~l~~~~~~~~~r~~----~~~~~HiTL~flg~~~~---------~~~~~l~~~l~~~~~~~~~f~~~~~~~ 74 (87)
T PF02834_consen 8 KEQLNQLQERLRQALPPLGIRWV----RPFNPHITLAFLGEVPP---------DQLPELIEALANIASRFPPFTLTVDGF 74 (87)
T ss_dssp HHHHHHHHHHHHHHCCSCTEEEG----SCGGSEEEEEEEEEESH---------HHHHHHHHHHHHHHCCCB-EEEEEEEE
T ss_pred HHHHHHHHHHHhhhccccCCccc----CCCCCeEEEEeCCCCCH---------HHHHHHHHHHHhhhccCCCeEEEEeEE
Confidence 36788888888888888899874 79999999999864321 1133444444433 233 4789999
Q ss_pred EEEeeecCCCCCce
Q 017090 349 HLSQRFVYDESGFY 362 (377)
Q Consensus 349 ~Ls~~~~~~~~g~Y 362 (377)
.++.+.. .++..|
T Consensus 75 ~~f~s~~-~~rvi~ 87 (87)
T PF02834_consen 75 GLFPSRL-RPRVIW 87 (87)
T ss_dssp EEEEEEE-TCEEEE
T ss_pred EEeCCCC-CCCCcC
Confidence 9976544 334444
No 52
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=96.50 E-value=0.0048 Score=58.03 Aligned_cols=64 Identities=25% Similarity=0.342 Sum_probs=54.7
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhh
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~ 85 (377)
.-+.||+.++..+||++|++++-|.++|+|+|-+-. +|-|.|.|++.....-|...|..+-.++
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~---NG~IWV~~~~~~~e~~~~~aI~~ie~ea 211 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ---NGRIWVDGENESLEELAIEAIRKIEREA 211 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec---CCEEEecCCCcchHHHHHHHHHHHhhhh
Confidence 457899999999999999999999999999999954 8999999987656777777777665553
No 53
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.47 E-value=0.0037 Score=46.64 Aligned_cols=36 Identities=22% Similarity=0.238 Sum_probs=34.0
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
....+.||++.++..||++|.+++.+++.+|.+|+|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678899999999999999999999999999999886
No 54
>PRK12705 hypothetical protein; Provisional
Probab=96.18 E-value=0.0062 Score=63.65 Aligned_cols=66 Identities=20% Similarity=0.340 Sum_probs=57.0
Q ss_pred EEEEEeCc-cccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhh
Q 017090 18 VLDMQVGA-SVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 18 ~~~i~Vp~-~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~ 85 (377)
+-.+.+|. ++-|.|||+.|++||.+|..||+.|.|++. .+.|+|.+-++..-+.|+..++.++...
T Consensus 199 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt--p~~V~ls~fdp~rreia~~~l~~Li~dg 265 (508)
T PRK12705 199 VSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT--PEAVVISSFNPIRREIARLTLEKLLADG 265 (508)
T ss_pred eeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC--ccchhhcccCccchHHHHHHHHHHHhcC
Confidence 55778888 678999999999999999999999999863 4578899988888889999998888764
No 55
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=96.01 E-value=0.087 Score=48.48 Aligned_cols=138 Identities=17% Similarity=0.194 Sum_probs=65.3
Q ss_pred eEEeec-cccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEcccc----CCCCCCCCceEEEEeeeccCChhHHHHHH
Q 017090 206 HLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLD----LMRGSKDKARILYAPVEEIGDGDRLLHAC 280 (377)
Q Consensus 206 HLTL~f-Lgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~----~F~~dp~~~rVLya~v~~~~~~~~L~~l~ 280 (377)
|+||.- +.+.+.+++ .+.|+++...+..+ ....+.++|+++. +| +=+|+.++. +..|..++
T Consensus 40 HiTL~s~i~~~~~~~~---~~~L~~~~~~~~~~-~~~~~~v~~~~v~~g~~yf-------q~vyl~v~~---t~~L~~l~ 105 (196)
T PF07823_consen 40 HITLTSGISLDSSDDV---QKVLDSAAAALKPL-PKNHFTVRFDKVASGDKYF-------QCVYLEVEK---TPELMSLA 105 (196)
T ss_dssp -EEEEEEEEE--HHHH---HHHHHHHHHH-B-E------EEEEEEEEEEEETT-------EEEEEEE------HHHHHHH
T ss_pred eEEEeCCCccCCHHHH---HHHHHHHHHhccCc-ccceeEEEeeeEeeCCeEE-------EEEEEEecC---ChhHHHHH
Confidence 999987 333334444 45566654432211 1111378887664 44 558999986 37899999
Q ss_pred HHHHHHHHHC-------CCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHhCCC-------ccccEEec
Q 017090 281 QVIIDAFNEA-------GLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFGSK-------EWGEYLIK 346 (377)
Q Consensus 281 ~~l~~~f~~~-------Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~~~~-------~fG~~~v~ 346 (377)
+.+++.|... |-. ...+|.||+.|+..--.... + -.++.+.....+. ..+.|.+.
T Consensus 106 ~~~r~~~~~~~~~~~~~~~~----~~~~y~PHlSLlY~d~~~~e----~---~~~~~~~~~i~~~l~~~~~~~~~~~~~~ 174 (196)
T PF07823_consen 106 QIARELFVEGPPDEVKAAEW----PREPYMPHLSLLYGDLPPEE----K---AEAAEIAQRIDDALGVDSGISGLGWEGG 174 (196)
T ss_dssp CHHHHCT----------T--------S----EEEEE-----HHH----H---HHHHHHHHHH-TT------GTT-EEEEE
T ss_pred HHHHHHhhhccccccccccc----cCCCCCCeEEEEEcCCCccc----H---HHHHHHHHHhcccccccccCCCCCEecc
Confidence 9999988542 121 25689999999975311100 0 0122344444443 34477899
Q ss_pred EEEEEeeecCCCCCceeEeEEEeC
Q 017090 347 EAHLSQRFVYDESGFYHCCASIPF 370 (377)
Q Consensus 347 ~I~Ls~~~~~~~~g~Y~~l~si~L 370 (377)
+|.|.... ++=.-..++++++|
T Consensus 175 ~l~lv~t~--g~v~~W~~l~~~~l 196 (196)
T PF07823_consen 175 ELKLVRTD--GPVEEWEVLASVDL 196 (196)
T ss_dssp EEEEEE----TT-TT-EEEEEEE-
T ss_pred EEEEEEcC--CCCCcEEEEEEEeC
Confidence 99996543 22356788888765
No 56
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.60 E-value=0.0026 Score=62.13 Aligned_cols=153 Identities=14% Similarity=0.100 Sum_probs=105.6
Q ss_pred CcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHH
Q 017090 203 KTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQV 282 (377)
Q Consensus 203 ~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~ 282 (377)
.++|+|+...-.+++.+++.-...|++....+..++...-...-|+|.++|+- .|-.+++... +.+++.++.
T Consensus 128 ~s~p~thflal~lne~eVqe~f~~fke~~~~~esl~~~g~~~s~F~~p~~~HL-----Tvgm~~L~~d---d~vq~a~e~ 199 (345)
T KOG2814|consen 128 KSFPITHFLALPLNEHEVQEGFLAFKELKPFIESLLDGGIDKSLFQGPGTFHL-----TVGMLKLLND---DDVQKALEI 199 (345)
T ss_pred hcCchhhhhhhhcchHHHHHHHHHHHhhhhhHHHhhccchhhccccCCceeeE-----EEEEEEecCh---HHHHHHHHH
Confidence 58999999998999999999998998665554454555555666789999987 7888888753 678888999
Q ss_pred HHHHHHHCCCcccccCCCCeeeeEEeeeeccc--ccccCCCccccccHHHHHHHhCCCccccEEecEEEEEeeecCCC-C
Q 017090 283 IIDAFNEAGLVFHRDYNKKLKLHATLMNIRHK--KRRKGTRRVDYFDARDIFKQFGSKEWGEYLIKEAHLSQRFVYDE-S 359 (377)
Q Consensus 283 l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~--~~~~~~~~~~~fda~~il~~~~~~~fG~~~v~~I~Ls~~~~~~~-~ 359 (377)
+...|.+.+...+ +..-|.+|-+++..... ...-.+.+..+-+..+.+ +..+|.+....++.|.+...+. .
T Consensus 200 les~~~e~~~~~~--~kp~~i~lkG~~~mnddP~~~kVLYAkv~~~~~e~~l----~~~~~~~i~~~f~~~~li~k~~~~ 273 (345)
T KOG2814|consen 200 LESTFQEIRIDVG--EKPLFIDLKGLDKMNDDPSLTKVLYAKVEPDDYEKFL----QHRCGERILERFVASGLIKKESSS 273 (345)
T ss_pred HHHHHHHHHhccC--CCceeeeccchhhhcCCHhHheeeeeeccCcchHHHH----HHHHHHHHHHHHHHhcchhccccc
Confidence 9999999888876 36779999999887542 111112233333333333 3346666777777777655432 4
Q ss_pred CceeEeEEEe
Q 017090 360 GFYHCCASIP 369 (377)
Q Consensus 360 g~Y~~l~si~ 369 (377)
.+|||.....
T Consensus 274 ~kLH~TvmNs 283 (345)
T KOG2814|consen 274 LKLHCTVMNS 283 (345)
T ss_pred cEEEEEEehh
Confidence 6777765433
No 57
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=95.55 E-value=0.037 Score=52.71 Aligned_cols=64 Identities=17% Similarity=0.312 Sum_probs=48.0
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEeCCHHHHHHHHHHHHHHH
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAII 82 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~-~~~v~I~g~~~~~v~~A~~~I~~iv 82 (377)
.+.+-+.+.-.|.|||+||++||+|..++++.|++|.++. +..++|++. .+.|-.-...|.--+
T Consensus 49 e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad-~~ti~~ilk~iip~l 113 (390)
T KOG2192|consen 49 ELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISAD-IETIGEILKKIIPTL 113 (390)
T ss_pred eEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEecc-HHHHHHHHHHHhhhh
Confidence 4556677888999999999999999999999999998654 456788874 445544444443333
No 58
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=95.22 E-value=0.029 Score=58.47 Aligned_cols=104 Identities=26% Similarity=0.236 Sum_probs=73.9
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCC--CC-CCcEEEEe--------CCHHHHHHHHHHHHHHHHh---
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSS--KK-EDSIIIEG--------NSTDSVAKASEKIQAIIAE--- 84 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~--~~-~~~v~I~g--------~~~~~v~~A~~~I~~iv~~--- 84 (377)
..+-.+....|.|||++|.++++|..+|+++|+|-.. +. +..|+|+| +..+.+.+|.++|-...++
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~d~~ 124 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEEDDE 124 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccccccc
Confidence 5677888999999999999999999999888888554 22 57789999 1357899999988764221
Q ss_pred -hhc----CCCCCceeEEEeccccchhhhccHHHHHHHHhccc
Q 017090 85 -AVE----SPSLDYSHFVSLPLAVHPELVDKLVNFQNTILGIT 122 (377)
Q Consensus 85 -~~~----~~~~~~~~fv~~Pl~~~p~I~~~~~~f~~~Il~~~ 122 (377)
... ......+-=+-+|-+.--.|+|+.+..+++|.++.
T Consensus 125 ~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~T 167 (485)
T KOG2190|consen 125 AAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREET 167 (485)
T ss_pred ccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhc
Confidence 111 01111223344566545778999999999998763
No 59
>TIGR03223 Phn_opern_protn putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model "Protein of unknown function (DUF1045)" which contains proteins found in a different genomic context as well.
Probab=93.19 E-value=1.4 Score=41.63 Aligned_cols=143 Identities=12% Similarity=0.120 Sum_probs=80.3
Q ss_pred CcceEEeec-cccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEE---EEccccCCCCCCCCceEEEEeeeccCChhHHHH
Q 017090 203 KTFHLTVLM-LKLWNKDRVNAATNVLKSISSKVMDALDNRPLFI---RLKGLDLMRGSKDKARILYAPVEEIGDGDRLLH 278 (377)
Q Consensus 203 ~~LHLTL~f-Lgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l---~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~ 278 (377)
--||.||+- +.+.+........++++.+... ..||.+ .+.-||-|- -+..+ .....|+.
T Consensus 56 YGfHaTLKaPFrLa~g~~~a~L~~al~~fA~~------~~pf~i~~L~l~~Lg~Fl--------AL~P~---~~~~~L~~ 118 (228)
T TIGR03223 56 YGFHATLKAPFRLAPGVTEAELLAAVAAFAAT------RAPFALPPLRVALLGGFL--------ALRPA---APCPALQA 118 (228)
T ss_pred cccceeecCCcccCCCCCHHHHHHHHHHHHhc------CCCccCCcceeeeeCCEE--------EEeeC---CCCHHHHH
Confidence 458999974 4554433344444555554332 345543 444554442 12222 34588999
Q ss_pred HHHHHHHHHHHC---------------CCccccc----------CCCCeeeeEEeeeecccccccCCCccccccHHHHHH
Q 017090 279 ACQVIIDAFNEA---------------GLVFHRD----------YNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFK 333 (377)
Q Consensus 279 l~~~l~~~f~~~---------------Gl~~~~~----------~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~ 333 (377)
|+..+.+.|... ||...++ --+.|..||||-..-..... . .+...++
T Consensus 119 LAa~~V~~~d~fRAPls~aelaRRr~~~Ls~~Q~~~L~~WGYPYV~deFrFHmTLTg~l~~~~~----~----~~~~~l~ 190 (228)
T TIGR03223 119 LAAACVRELDPFRAPLTEAELARRRPDQLTPRQRALLERWGYPYVLEEFRFHMTLTGRLDEEER----A----AVLARLE 190 (228)
T ss_pred HHHHHHHhhhhccCCCCHHHHhhcCccCCCHHHHHHHHHcCCCceecceEEEEEecCCCChHHH----H----HHHHHHH
Confidence 999999988432 2222110 02579999999864321100 0 1123333
Q ss_pred H-hCCCccccEEecEEEEEeeecCCCCCceeEeEEEeCCC
Q 017090 334 Q-FGSKEWGEYLIKEAHLSQRFVYDESGFYHCCASIPFPE 372 (377)
Q Consensus 334 ~-~~~~~fG~~~v~~I~Ls~~~~~~~~g~Y~~l~si~L~~ 372 (377)
. |...--..+.|+.|.|+.-. ..+.-++.+..++|++
T Consensus 191 ~~~~~~l~~p~~id~laLf~e~--~~g~pF~~~~~~~l~~ 228 (228)
T TIGR03223 191 ARFAPLLADPLAVDGLALFVEP--EPGAPFRLIARVALAG 228 (228)
T ss_pred HHhhhccCCCeeeeeEEEEecc--CCCCCcEEEEeecCCC
Confidence 3 34444457889999996542 2345699999999863
No 60
>PRK02821 hypothetical protein; Provisional
Probab=92.59 E-value=0.13 Score=40.37 Aligned_cols=32 Identities=16% Similarity=0.246 Sum_probs=27.8
Q ss_pred cceEEEEEeCccccccccCCCchhHHHHHHHh
Q 017090 15 SLSVLDMQVGASVIRFIKGKEGSTQKKFEKEM 46 (377)
Q Consensus 15 ~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et 46 (377)
....+.+.|.++-+|.|||++|++++.|..=-
T Consensus 29 ~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv 60 (77)
T PRK02821 29 RGRTLEVRVHPDDLGKVIGRGGRTATALRTVV 60 (77)
T ss_pred CcEEEEEEEChhhCcceeCCCCchHHHHHHHH
Confidence 44578999999999999999999999987653
No 61
>PRK00468 hypothetical protein; Provisional
Probab=92.46 E-value=0.14 Score=39.90 Aligned_cols=31 Identities=19% Similarity=0.339 Sum_probs=26.7
Q ss_pred cceEEEEEeCccccccccCCCchhHHHHHHH
Q 017090 15 SLSVLDMQVGASVIRFIKGKEGSTQKKFEKE 45 (377)
Q Consensus 15 ~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~e 45 (377)
......+.+.++-+|.|||++|+|++.|..=
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 3457789999999999999999999998653
No 62
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=92.19 E-value=0.11 Score=57.26 Aligned_cols=38 Identities=29% Similarity=0.633 Sum_probs=36.4
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCC
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 54 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~ 54 (377)
-..++.||.++|+.|||++|.+.|.++.+++|.|.+|.
T Consensus 709 ~~~~~~~p~~~~~~~ig~~g~~~r~~~~~~~~~~~~~~ 746 (753)
T KOG2208|consen 709 VTKEIEIPRSLHRYLIGPKGSNLRQLEKEFNVNIVVPN 746 (753)
T ss_pred eeeEEeccHHHhhhccCCCCccHHHHHHHhccceecCC
Confidence 37899999999999999999999999999999999997
No 63
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=92.06 E-value=0.16 Score=39.73 Aligned_cols=31 Identities=16% Similarity=0.289 Sum_probs=26.9
Q ss_pred ccceEEEEEeCccccccccCCCchhHHHHHH
Q 017090 14 ISLSVLDMQVGASVIRFIKGKEGSTQKKFEK 44 (377)
Q Consensus 14 ~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~ 44 (377)
.+.-...+.|.++-+|.|||++|+|++.|..
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRT 57 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRT 57 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHH
Confidence 3445789999999999999999999999864
No 64
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=91.96 E-value=0.1 Score=47.77 Aligned_cols=53 Identities=26% Similarity=0.360 Sum_probs=45.9
Q ss_pred ccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 27 VIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 27 ~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
-||.|+|++|+|.=.||+-|.++|.+.. ..|-|-|. -+++.-|++.|-.++-.
T Consensus 179 AIGRiaGk~GkTkfaIEn~trtrIVlad----~kIHiLG~-~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 179 AIGRIAGKGGKTKFAIENVTRTRIVLAD----SKIHILGA-FQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHhhcCCCcceeeeeccceeEEEecC----ceEEEeec-chhhHHHHHhhHhhhcc
Confidence 4899999999999999999999999963 67999996 46899999988877754
No 65
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.23 E-value=0.11 Score=39.81 Aligned_cols=35 Identities=11% Similarity=0.116 Sum_probs=29.6
Q ss_pred ccceEEEEEeCccccccccCCCchhHHHHHHHhCc
Q 017090 14 ISLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGV 48 (377)
Q Consensus 14 ~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~ 48 (377)
.......+.+..+-.|.|||++|+|++.|+.=++.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 34557889999999999999999999999876543
No 66
>PRK01064 hypothetical protein; Provisional
Probab=90.96 E-value=0.27 Score=38.67 Aligned_cols=33 Identities=27% Similarity=0.325 Sum_probs=28.3
Q ss_pred ccceEEEEEeCccccccccCCCchhHHHHHHHh
Q 017090 14 ISLSVLDMQVGASVIRFIKGKEGSTQKKFEKEM 46 (377)
Q Consensus 14 ~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et 46 (377)
.+.....+.|.++-.|.+||++|+|++.|..=.
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 455578899999999999999999999987643
No 67
>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=90.83 E-value=0.35 Score=35.46 Aligned_cols=34 Identities=15% Similarity=0.213 Sum_probs=27.7
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEE
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKI 50 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I 50 (377)
....+.+.....|.+||++|++++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4556666666689999999999999999999554
No 68
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=90.80 E-value=0.18 Score=51.99 Aligned_cols=41 Identities=27% Similarity=0.357 Sum_probs=36.8
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 57 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~ 57 (377)
....+.||...++.+||++|+++++||+..|.+|++-..++
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 35789999999999999999999999999999999965444
No 69
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=90.68 E-value=0.9 Score=41.88 Aligned_cols=66 Identities=18% Similarity=0.261 Sum_probs=56.4
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhh
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAV 86 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~ 86 (377)
.+.+.+++..+-+|...+|..++.|-...|++|.+.. +.+.|.|+|+ +..++.+...|..++...+
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~--~~~~i~I~g~-k~~~~~i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR--SENRIRITGT-KSTAEYIEASINEILSNIR 92 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec--CCcEEEEEcc-HHHHHHHHHHHHHHHhhcE
Confidence 4567778999999999999999999888899999976 3679999996 6789999999998887643
No 70
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=90.62 E-value=0.31 Score=42.56 Aligned_cols=41 Identities=12% Similarity=0.030 Sum_probs=36.2
Q ss_pred cccceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcC
Q 017090 13 LISLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 53 (377)
Q Consensus 13 ~~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip 53 (377)
-.+.....+.|+++..|..||++|.|++.++.-+|-.++|.
T Consensus 95 ~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 95 KNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred cCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 33446778899999999999999999999999999999884
No 71
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=90.57 E-value=0.17 Score=52.79 Aligned_cols=97 Identities=23% Similarity=0.347 Sum_probs=67.0
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC-CCcEEEEeCCHHHHHHHHHHHHHHHHhhhcCCCCCceeE
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK-EDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHF 96 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~-~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~~~~~~~~f 96 (377)
.+++-||.++...+||++|.+++.|+..|+.+|.+...+. ...+-+.+.-...+..|+..|-.++.+.. ++..=
T Consensus 69 ~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~-----pvk~~ 143 (608)
T KOG2279|consen 69 EIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVGDERVLLISGFPVQVCKAKAAIHQILTENT-----PVSEQ 143 (608)
T ss_pred eeeEeecccceeeeeccccCCcchhhcccccceecCcccCCcccchhhccCCCCCChHHHHHHHHHhcCC-----ccccc
Confidence 4678899999999999999999999999999999976443 33455555334567777776655554421 23333
Q ss_pred EEeccccchhhhccHHHHHHHHh
Q 017090 97 VSLPLAVHPELVDKLVNFQNTIL 119 (377)
Q Consensus 97 v~~Pl~~~p~I~~~~~~f~~~Il 119 (377)
.+.|...|+.|.++.+..++++-
T Consensus 144 lsvpqr~~~~i~grgget~~si~ 166 (608)
T KOG2279|consen 144 LSVPQRSVGRIIGRGGETIRSIC 166 (608)
T ss_pred ccchhhhcccccccchhhhcchh
Confidence 45566556667666666665553
No 72
>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=89.04 E-value=0.23 Score=38.40 Aligned_cols=40 Identities=25% Similarity=0.328 Sum_probs=32.9
Q ss_pred eccccceEEEEEeCccccccccCCCchhHHHHHHHhCcEEE
Q 017090 11 IDLISLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKII 51 (377)
Q Consensus 11 ~~~~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ 51 (377)
|+|.. ....+.+-.+.-+.+||++|+++++|.++.+-.+.
T Consensus 20 I~r~~-~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 20 IERTP-DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEESS-SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred EEEcC-CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 44433 66778888999999999999999999998877765
No 73
>PRK13764 ATPase; Provisional
Probab=88.74 E-value=0.32 Score=52.16 Aligned_cols=43 Identities=28% Similarity=0.281 Sum_probs=37.7
Q ss_pred cceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 017090 15 SLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 57 (377)
Q Consensus 15 ~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~ 57 (377)
+-....+.||...++.+|||||++|++||+..|..|+|-..++
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~ 521 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDE 521 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccc
Confidence 3447789999999999999999999999999999999965443
No 74
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=87.47 E-value=0.7 Score=40.34 Aligned_cols=86 Identities=20% Similarity=0.180 Sum_probs=53.4
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHHHhhhcC------CCC
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAIIAEAVES------PSL 91 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~------~~~ 91 (377)
..-+-|+....|..||++|+.++.|++..|-+|+|=.- .. .+.+.|..++..+... ...
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~---------s~------d~~~fI~n~l~Pa~V~~v~I~~~~~ 97 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY---------SD------DPEEFIKNIFAPAAVRSVTIKKKNG 97 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc---------CC------CHHHHHHHHcCCCEEEEEEEEecCC
Confidence 55667788899999999999999999999988887321 11 1233444443332210 001
Q ss_pred CceeEEEeccccchhhhccHHHHHHHH
Q 017090 92 DYSHFVSLPLAVHPELVDKLVNFQNTI 118 (377)
Q Consensus 92 ~~~~fv~~Pl~~~p~I~~~~~~f~~~I 118 (377)
....||-++-......+|+.++..+.+
T Consensus 98 ~~~~~V~V~~~d~g~aIGK~G~ni~la 124 (140)
T PRK08406 98 DKVAYVEVAPEDKGIAIGKNGKNIERA 124 (140)
T ss_pred cEEEEEEECccccchhhCCCCHHHHHH
Confidence 134566666555566666666655544
No 75
>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=86.98 E-value=0.58 Score=36.32 Aligned_cols=36 Identities=14% Similarity=0.269 Sum_probs=30.6
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
....+.|..+..|.+||+.|+|+..||-=++.-++-
T Consensus 24 ~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 24 DTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred CEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 367788999999999999999999999887765554
No 76
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=85.66 E-value=0.59 Score=45.70 Aligned_cols=65 Identities=20% Similarity=0.279 Sum_probs=55.7
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHH-HHHHHHH
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKAS-EKIQAII 82 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~-~~I~~iv 82 (377)
...+.+|....|.+.|++|++++.+++-|++.|.-|.+..+...-++|-...++++|+ ..|+..+
T Consensus 116 ~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~~~~Vf~Vtg~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 116 TSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRCGEPVFCVTGAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred ceeeeccceeeeeccccccCccchheecccceEeeeccCCCceEEEecCCcchhhhccccchhhhh
Confidence 5678899999999999999999999999999999998766677789997776788888 6666543
No 77
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=85.49 E-value=1.6 Score=42.18 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=38.5
Q ss_pred cccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHH
Q 017090 28 IRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQA 80 (377)
Q Consensus 28 ~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~ 80 (377)
.-.+|||+|.|++.||=-|+|-|-+- .++|.+.|+= .++..++..+..
T Consensus 160 RqRLiGpng~TLKAlelLT~CYilVq----G~TVsaiGpf-kGlkevr~IV~D 207 (356)
T KOG2874|consen 160 RQRLIGPNGSTLKALELLTNCYILVQ----GNTVSAIGPF-KGLKEVRKIVED 207 (356)
T ss_pred HHHhcCCCchhHHHHHHHhhcEEEee----CcEEEeecCc-chHHHHHHHHHH
Confidence 34689999999999999999999995 3789999974 477766654443
No 78
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=84.82 E-value=0.89 Score=34.80 Aligned_cols=26 Identities=35% Similarity=0.437 Sum_probs=22.1
Q ss_pred cccccCCCchhHHHHHHHh-CcEEEcC
Q 017090 28 IRFIKGKEGSTQKKFEKEM-GVKIILP 53 (377)
Q Consensus 28 ~~~iIG~~G~tik~ie~et-~~~I~ip 53 (377)
+|..||++|+.++.|+++. |-+|+|=
T Consensus 19 vG~~iG~~G~rik~i~~~L~gekIdvV 45 (69)
T PF13184_consen 19 VGACIGKKGSRIKAISEELNGEKIDVV 45 (69)
T ss_dssp HHHHH-CCCCCHHHHHHHTTT-EEEEE
T ss_pred ceecCccccHHHHHHHHHhCCCeEEEE
Confidence 8999999999999999999 8888873
No 79
>PHA02977 hypothetical protein; Provisional
Probab=84.01 E-value=3.9 Score=35.84 Aligned_cols=94 Identities=18% Similarity=0.161 Sum_probs=54.6
Q ss_pred eEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCC------CceEEEEeeeccCChhHHHHH
Q 017090 206 HLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKD------KARILYAPVEEIGDGDRLLHA 279 (377)
Q Consensus 206 HLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~------~~rVLya~v~~~~~~~~L~~l 279 (377)
|+||+.-.-...+..+.-++....+ .-..++++-+..-+||++.. +-+-+.++++.+ +.|..|
T Consensus 71 hitlgian~dq~~~f~~fk~~~~d~--------dl~sis~~cke~icfpqs~askelga~g~avvmkle~s---ddlkal 139 (201)
T PHA02977 71 HITLGIANKDQCDNFENFKELIKDI--------DLQSISFTCKEEICFPQSNASKELGAKGCAVVMKLEAS---DDLKAL 139 (201)
T ss_pred ceeeeccCccHhHHHHHHHHHhhcc--------cceeEEEEeeeeEeccccchhhhhCcCccEEEEEEEec---hHHHHH
Confidence 9999875433223333333332222 23667778888889986321 234566677654 567666
Q ss_pred HHHHHHHHH----HCCCcccccCCCCeeeeEEeeeecc
Q 017090 280 CQVIIDAFN----EAGLVFHRDYNKKLKLHATLMNIRH 313 (377)
Q Consensus 280 ~~~l~~~f~----~~Gl~~~~~~~r~fkpHiTL~r~~~ 313 (377)
.+.|-.+.- -.|=... ..+.-||+|+..++.
T Consensus 140 rnvl~n~vp~pkdifg~i~~---d~~w~phitigyv~~ 174 (201)
T PHA02977 140 RNVLFNAVPCPKDIFGDILS---DNPWCPHITIGYVKA 174 (201)
T ss_pred HHHhhcccCCcHHhhccccc---CCCCCCceEEEeecc
Confidence 666654321 1233332 368999999998864
No 80
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=82.09 E-value=1.7 Score=39.93 Aligned_cols=42 Identities=26% Similarity=0.262 Sum_probs=33.9
Q ss_pred eccccce-EEEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 11 IDLISLS-VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 11 ~~~~~~~-~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
+.|..++ ..+..+-.+-+|..||++|+.++.|.++.|-+|+|
T Consensus 69 i~rd~r~av~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdV 111 (190)
T COG0195 69 VARDPRAAVVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDV 111 (190)
T ss_pred EEeccccceEEeecCcCchhhhccCCChHHHHHHHHhCCceEE
Confidence 4555533 56777777889999999999999999999966665
No 81
>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=80.32 E-value=1.6 Score=38.14 Aligned_cols=38 Identities=13% Similarity=0.031 Sum_probs=34.4
Q ss_pred ceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcC
Q 017090 16 LSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 53 (377)
Q Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip 53 (377)
.....+.||++..+..||++|.+++...+-||-+++|.
T Consensus 99 ~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 99 KKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 34677999999999999999999999999999999884
No 82
>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=80.28 E-value=2.4 Score=37.10 Aligned_cols=36 Identities=25% Similarity=0.270 Sum_probs=32.0
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcC
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 53 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip 53 (377)
.+-+-|.+...|..||++|+.++.|++..|-+|+|=
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV 69 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI 69 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE
Confidence 567788999999999999999999988889888873
No 83
>PF10469 AKAP7_NLS: AKAP7 2'5' RNA ligase-like domain; InterPro: IPR019510 This entry represents the N-terminal nuclear localisation signal-containing domain found in the cyclic AMP-dependent protein kinase A (PKA) anchor protein, AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes []. This domain carries the nuclear localisation signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein []. Binding to the regulatory subunits RI and RII of PKA is mediated via the RI-RII subunit-binding domain at the C terminus.
Probab=79.67 E-value=0.36 Score=44.46 Aligned_cols=25 Identities=20% Similarity=0.272 Sum_probs=22.5
Q ss_pred ccceeEEEeecCCCccceecccccc
Q 017090 150 QEHKVAVELNIGDNSERVKVDRTSI 174 (377)
Q Consensus 150 ~~~fvav~~~~~~~~~~v~~~~~~~ 174 (377)
|||||||+|+.+++.++++.+|+.|
T Consensus 1 pthFl~ipl~~~~i~~~~~~fq~~v 25 (209)
T PF10469_consen 1 PTHFLCIPLNSPEIQEKFKEFQNEV 25 (209)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHH
Confidence 8999999999999999999888654
No 84
>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=79.23 E-value=1.3 Score=34.92 Aligned_cols=43 Identities=9% Similarity=0.271 Sum_probs=32.8
Q ss_pred eccccceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCC
Q 017090 11 IDLISLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 54 (377)
Q Consensus 11 ~~~~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~ 54 (377)
|.|.. ....+.|-..+-|.+||++|+++++|.++-.....++.
T Consensus 25 I~Rt~-~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 25 VRVTP-TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEcC-CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 44532 23666677777899999999999999998877777753
No 85
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=76.51 E-value=3.2 Score=37.29 Aligned_cols=35 Identities=23% Similarity=0.377 Sum_probs=29.2
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcC
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 53 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip 53 (377)
.+.+-|.+-. |.-||++|+++|++++..|-+|.+=
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 4455566666 9999999999999999999988873
No 86
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=76.31 E-value=2.8 Score=38.46 Aligned_cols=37 Identities=19% Similarity=0.199 Sum_probs=34.5
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCC
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 54 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~ 54 (377)
...+.||++..+..||++|.+++...+=||.+|+|-.
T Consensus 143 ~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 143 VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 6778899999999999999999999999999999954
No 87
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=73.70 E-value=3.7 Score=41.57 Aligned_cols=42 Identities=14% Similarity=-0.017 Sum_probs=37.4
Q ss_pred ceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC
Q 017090 16 LSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK 57 (377)
Q Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~ 57 (377)
.....+.||.+..+.-||++|.++|---+-||.+|+|-+-++
T Consensus 307 ~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 307 EKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred CcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 357788999999999999999999999999999999966443
No 88
>KOG3102 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.10 E-value=14 Score=34.50 Aligned_cols=101 Identities=11% Similarity=0.214 Sum_probs=68.6
Q ss_pred CCCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceE-EEEeeeccCChhHHHHH
Q 017090 201 KPKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHA 279 (377)
Q Consensus 201 ~p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rV-Lya~v~~~~~~~~L~~l 279 (377)
.-.-|||.|+=-.-+.--+|.....+|++-.. ....|-+++.++.+|-+ .++.|. +-+.+.. .+...+.++
T Consensus 118 ~~~~fHlSLsr~VvLr~HqI~~fi~~L~~~l~------s~~rf~~t~n~~~iytN-~e~TRtFi~leitt-~~~~~~~~~ 189 (269)
T KOG3102|consen 118 LGREFHLSLSRNVVLRVHQINSFISMLRQKLQ------SQKRFLITFNKWEIYTN-DEHTRTFISLEITT-SGLSEISKQ 189 (269)
T ss_pred ccceEEEeeccceEEEeehhhHHHHHHHHHHh------hhhhheEeecceEEEec-cccceeEEEEEech-hhHHHHHHH
Confidence 35789999975444444566666666655321 24678999999999987 455565 3344543 456677777
Q ss_pred HHHHHHHHHHCCCcccccCCCCeeeeEEeeeec
Q 017090 280 CQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIR 312 (377)
Q Consensus 280 ~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~ 312 (377)
.+.+.+.+....|..- ..+| .+|+.|+=.-
T Consensus 190 i~~vd~Vm~~~nL~~F--Y~DP-sfHiSL~Wcv 219 (269)
T KOG3102|consen 190 IDAVDEVMKLHNLPEF--YKDP-SFHISLVWCV 219 (269)
T ss_pred HHHHHHHHHHcCchhh--hcCC-CCCceEEEEe
Confidence 8888888888888753 2345 9999998653
No 89
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=71.09 E-value=3.1 Score=43.47 Aligned_cols=67 Identities=16% Similarity=0.207 Sum_probs=51.3
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC------CCcEEEEeC--CHHHHHHHHHHHHHHHHh
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK------EDSIIIEGN--STDSVAKASEKIQAIIAE 84 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~------~~~v~I~g~--~~~~v~~A~~~I~~iv~~ 84 (377)
.+++-||..-|..|||.||..+++....-++-|++-..-+ .+.|.|.+| +..++..++.-...+|.+
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ni~~~KNd~~~~V~~ 524 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQDNISGKKNDKLDKVKQ 524 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCccchhcccccHHHHHhh
Confidence 5788999999999999999999999999998888743211 245888885 556666777666666664
No 90
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=69.66 E-value=4.2 Score=33.75 Aligned_cols=33 Identities=21% Similarity=0.354 Sum_probs=26.9
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEE
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKI 50 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I 50 (377)
...+.|-..+-|.|||++|+++++|++.....+
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~ 94 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQKLL 94 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHHHh
Confidence 466777777889999999999999988866543
No 91
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=67.62 E-value=5.9 Score=40.01 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=36.1
Q ss_pred ceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCC
Q 017090 16 LSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 54 (377)
Q Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~ 54 (377)
.....+.||.+..+.-||++|.++|--..-||.+|+|-+
T Consensus 302 ~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s 340 (362)
T PRK12327 302 EKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKS 340 (362)
T ss_pred CcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEE
Confidence 357889999999999999999999999999999999965
No 92
>PLN00108 unknown protein; Provisional
Probab=67.32 E-value=1.1 Score=42.88 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=26.2
Q ss_pred hhccccceeEEEee-cCCCccceecccccc
Q 017090 146 QQVDQEHKVAVELN-IGDNSERVKVDRTSI 174 (377)
Q Consensus 146 ~~~r~~~fvav~~~-~~~~~~~v~~~~~~~ 174 (377)
++..+||||||+|+ .|++.++++++++++
T Consensus 32 ~~~~~THFlavPL~~~p~i~~~~~~Fk~~V 61 (257)
T PLN00108 32 HREVFTHFVSLPLAIYPDLKKNIEAFQNSV 61 (257)
T ss_pred cCCCCCeEEEEEcCCCHHHHHHHHHHHHHH
Confidence 36789999999996 899999999999877
No 93
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=67.13 E-value=5.5 Score=41.66 Aligned_cols=38 Identities=24% Similarity=0.253 Sum_probs=35.3
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCC
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 54 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~ 54 (377)
....+-||.+..+.-||++|.++|...+-||.+|+|=+
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 47889999999999999999999999999999999954
No 94
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=65.02 E-value=6.2 Score=34.66 Aligned_cols=36 Identities=22% Similarity=0.267 Sum_probs=29.9
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcC
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 53 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip 53 (377)
+-.+.|-.++=|.+||++|.++++|-.+||-+-.|-
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vv 112 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVV 112 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEE
Confidence 345666677889999999999999999999776663
No 95
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=61.53 E-value=15 Score=28.87 Aligned_cols=36 Identities=31% Similarity=0.439 Sum_probs=29.6
Q ss_pred hCcEEEcCCCCCCCcEEEEeC-CHHHHHHHHHHHHHHHHh
Q 017090 46 MGVKIILPSSKKEDSIIIEGN-STDSVAKASEKIQAIIAE 84 (377)
Q Consensus 46 t~~~I~ip~~~~~~~v~I~g~-~~~~v~~A~~~I~~iv~~ 84 (377)
.+|.+.|=+ +|.|+|+|. +.+.+.+|.++|..++.+
T Consensus 48 p~~t~~IF~---sGki~itGaks~~~~~~a~~~i~~~L~~ 84 (86)
T PF00352_consen 48 PKATVLIFS---SGKIVITGAKSEEEAKKAIEKILPILQK 84 (86)
T ss_dssp TTEEEEEET---TSEEEEEEESSHHHHHHHHHHHHHHHHH
T ss_pred CcEEEEEEc---CCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 356777755 799999995 899999999999988865
No 96
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=61.47 E-value=9.7 Score=39.39 Aligned_cols=39 Identities=21% Similarity=0.192 Sum_probs=35.9
Q ss_pred ceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCC
Q 017090 16 LSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPS 54 (377)
Q Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~ 54 (377)
.....+.||.+..+.-||++|.++|---.-||.+|+|-+
T Consensus 334 ~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 334 GRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 356789999999999999999999999999999999964
No 97
>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=60.21 E-value=9.5 Score=30.08 Aligned_cols=29 Identities=10% Similarity=0.242 Sum_probs=22.4
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhC
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMG 47 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~ 47 (377)
..+.|-..+-|.+||++|+++++|.+.-.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence 44455557889999999999999877654
No 98
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=59.03 E-value=12 Score=38.06 Aligned_cols=45 Identities=18% Similarity=0.094 Sum_probs=35.6
Q ss_pred ceeccccceEEEEEe-----CccccccccCCCchhHHHHHHHh-CcEEEcC
Q 017090 9 KFIDLISLSVLDMQV-----GASVIRFIKGKEGSTQKKFEKEM-GVKIILP 53 (377)
Q Consensus 9 ~~~~~~~~~~~~i~V-----p~~~~~~iIG~~G~tik~ie~et-~~~I~ip 53 (377)
+-|+|.++..-.+-| .-+-+|..||++|..++.|.++. |=+|+|=
T Consensus 229 k~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 229 IHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred EEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 457888888555554 33569999999999999999998 7777763
No 99
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=57.73 E-value=13 Score=37.61 Aligned_cols=45 Identities=20% Similarity=0.152 Sum_probs=35.0
Q ss_pred ceeccccceEEEEEeCc-----cccccccCCCchhHHHHHHHh-CcEEEcC
Q 017090 9 KFIDLISLSVLDMQVGA-----SVIRFIKGKEGSTQKKFEKEM-GVKIILP 53 (377)
Q Consensus 9 ~~~~~~~~~~~~i~Vp~-----~~~~~iIG~~G~tik~ie~et-~~~I~ip 53 (377)
+-|+|.++..-.+-|-+ +-+|..||++|..++.|.++. |-+|+|=
T Consensus 223 k~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv 273 (362)
T PRK12327 223 KSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDII 273 (362)
T ss_pred EEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhCCCeEEEE
Confidence 45788888755554422 558999999999999999998 7788773
No 100
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=56.21 E-value=6 Score=41.63 Aligned_cols=67 Identities=25% Similarity=0.280 Sum_probs=51.5
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCC---CcEEEEeCCHHHHHHHHHHHHHHHHh
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKE---DSIIIEGNSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~---~~v~I~g~~~~~v~~A~~~I~~iv~~ 84 (377)
......+|...++.|+|+||.|++.|+.-.+.+|.+...+.. ..+.|.+. ..-+..|+..|..=+.+
T Consensus 140 vk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~q-qk~~~~a~~~~~~~~~e 209 (608)
T KOG2279|consen 140 VSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQ-QKEVAAAKHLILEKVSE 209 (608)
T ss_pred ccccccchhhhcccccccchhhhcchhcccccccccccccccccccceecccc-cchHHHHHhhhhccccc
Confidence 367788999999999999999999999999999999875543 23455443 44566777777665544
No 101
>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=55.48 E-value=15 Score=36.93 Aligned_cols=45 Identities=24% Similarity=0.179 Sum_probs=34.7
Q ss_pred ceeccccceEEEEEeC-----ccccccccCCCchhHHHHHHHh-CcEEEcC
Q 017090 9 KFIDLISLSVLDMQVG-----ASVIRFIKGKEGSTQKKFEKEM-GVKIILP 53 (377)
Q Consensus 9 ~~~~~~~~~~~~i~Vp-----~~~~~~iIG~~G~tik~ie~et-~~~I~ip 53 (377)
+-|+|.++....+-|- -+-+|..||++|..++.|.++. |=+|+|=
T Consensus 221 ~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv 271 (341)
T TIGR01953 221 KKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELNGEKIDII 271 (341)
T ss_pred EEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhCCCeEEEE
Confidence 4578888875544442 2559999999999999999998 7777763
No 102
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=54.57 E-value=12 Score=35.28 Aligned_cols=71 Identities=15% Similarity=0.236 Sum_probs=44.6
Q ss_pred ccccceeEEEeecCCCccceecccccccccccccccCCCCCCCCCCCCccccc-CCCcceEEeeccccCCHHHHHHH-HH
Q 017090 148 VDQEHKVAVELNIGDNSERVKVDRTSIPIVGYEAKASRPSTSSDLGIDKSIFI-KPKTFHLTVLMLKLWNKDRVNAA-TN 225 (377)
Q Consensus 148 ~r~~~fvav~~~~~~~~~~v~~~~~~~~~~~~~~~~~r~~~~~~~gi~~~~~v-~p~~LHLTL~fLgl~~~~~v~~a-~~ 225 (377)
.+...|+|++|..+.... ++...+.+ ..++..+|+++ |. ....+|+.|+..-....+++.+. .+
T Consensus 138 e~TR~FL~l~V~~~~~~~-l~~l~~~i-----------~~~l~~~~lp~--~Y~~~~~fHvSIAw~~~~~~~~l~~~~~~ 203 (239)
T PF09749_consen 138 EKTRSFLALRVSEGSNNE-LKRLLDRI-----------NEVLKEFGLPP--FYDEDPSFHVSIAWTLGDPSEELKESSLK 203 (239)
T ss_pred CCCeEEEEEEecccccHH-HHHHHHHH-----------HHHHHHhCCCc--ccCCCCCCEEEEEEECCCchHHHHHHHHH
Confidence 345799999999876543 55555444 12344566555 44 88999999998754445555544 35
Q ss_pred HHHHhHH
Q 017090 226 VLKSISS 232 (377)
Q Consensus 226 ~L~~i~~ 232 (377)
.+..+..
T Consensus 204 ~~~~~~~ 210 (239)
T PF09749_consen 204 ILQEPLD 210 (239)
T ss_pred HHHHHHh
Confidence 5555533
No 103
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=51.92 E-value=39 Score=33.93 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=44.8
Q ss_pred CccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHH
Q 017090 24 GASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAI 81 (377)
Q Consensus 24 p~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~i 81 (377)
+....-.+.|+.|.+++.|++.+|+.|.-+. ..+.|.|.. ..++.|...++.+
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG----~~~~i~g~~-~~v~~A~~~l~~l 74 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG----EAVRIIGAR-PLVDVATRVLLTL 74 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC----ceEEEEech-HHHHHHHHHHhHH
Confidence 4567788999999999999999999998763 578999974 4999999999843
No 104
>PF07823 CPDase: Cyclic phosphodiesterase-like protein; InterPro: IPR012386 2',3' Cyclic nucleotide phosphodiesterases (CPDases) are enzymes that catalyse at least two distinct steps in the splicing of tRNA introns in eukaryotes. The active site is characterised by two conserved histidine residues []. The enzyme has six cysteine residues, four of which are involved in forming two intra-molecular disulphide bridges. One of these bridges is involved in the catalytic activity of the enzyme as it opens when CPDase is semi-reduced []. Proteins in this entryand belong to 3.1.4.37 from EC and catalyse the reaction Nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 2'-phosphate. ; GO: 0004112 cyclic-nucleotide phosphodiesterase activity; PDB: 1JH7_A 1JH6_B 1FSI_B.
Probab=50.63 E-value=17 Score=33.31 Aligned_cols=42 Identities=17% Similarity=0.074 Sum_probs=19.2
Q ss_pred EEEEeeec-cCChhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeeee
Q 017090 262 ILYAPVEE-IGDGDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNI 311 (377)
Q Consensus 262 VLya~v~~-~~~~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~ 311 (377)
-||+-+.. ++....|+.+-..|...|-.. .-.|-||+||.-.
T Consensus 4 SlWl~P~~~~~~~~~L~~lI~~L~~~~~~~--------~p~F~PHiTL~s~ 46 (196)
T PF07823_consen 4 SLWLVPPPGSPLYERLKTLISSLASLFPGS--------PPPFEPHITLTSG 46 (196)
T ss_dssp EEEEEE-T--TTHHHHHHHHHHHHHHST-----------------EEEEEE
T ss_pred EEEEcCCCCccHHHHHHHHHHHHHHHCCCC--------CCCcCCeEEEeCC
Confidence 37776654 233456666665555543311 1479999999974
No 105
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=50.41 E-value=13 Score=35.10 Aligned_cols=35 Identities=23% Similarity=0.229 Sum_probs=25.5
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
...|.|-...=|.|||++|+.|++|.++....+..
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~ 86 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGK 86 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCC
Confidence 44555566778999999999999987765544433
No 106
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=47.73 E-value=99 Score=26.12 Aligned_cols=61 Identities=11% Similarity=0.146 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 017090 219 RVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 294 (377)
Q Consensus 219 ~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~ 294 (377)
.++.+.++|.+.+ ......|.++|..++-+ ..+.+ ...+...+..+++.+.+.+.++|+.+
T Consensus 6 l~~~i~~alddkK-------AeDIv~lDv~~~s~~tD-----yfVIa---tg~s~rhv~Aiad~i~~~~k~~g~~~ 66 (115)
T COG0799 6 LLEVIVEALDDKK-------AEDIVVLDVSGKSSLTD-----YFVIA---TGNSSRHVKAIADNVKEELKEAGEVP 66 (115)
T ss_pred HHHHHHHHHHhcc-------CCCeEEEEccCCccccc-----EEEEE---EeCchHHHHHHHHHHHHHHHHcCCCc
Confidence 3444555555543 34678899999999987 34433 32335789999999999999998876
No 107
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=46.30 E-value=23 Score=37.08 Aligned_cols=46 Identities=24% Similarity=0.169 Sum_probs=35.7
Q ss_pred cceeccccceEEEEEeCc-----cccccccCCCchhHHHHHHHh-CcEEEcC
Q 017090 8 PKFIDLISLSVLDMQVGA-----SVIRFIKGKEGSTQKKFEKEM-GVKIILP 53 (377)
Q Consensus 8 ~~~~~~~~~~~~~i~Vp~-----~~~~~iIG~~G~tik~ie~et-~~~I~ip 53 (377)
=+-|+|.++..-.+-|-+ +=+|..||++|..++.|.++. |=+|+|=
T Consensus 222 Ik~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv 273 (470)
T PRK09202 222 IKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDII 273 (470)
T ss_pred EEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEE
Confidence 355788888855555422 458999999999999999998 7777763
No 108
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=45.88 E-value=17 Score=33.75 Aligned_cols=38 Identities=11% Similarity=0.038 Sum_probs=32.9
Q ss_pred cceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 15 SLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 15 ~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
....+.++|..+-.+.|||+.|+|+..||-=++.-++-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 44577888888889999999999999999999877765
No 109
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=43.21 E-value=84 Score=28.10 Aligned_cols=75 Identities=16% Similarity=0.140 Sum_probs=43.7
Q ss_pred CChhHHHHHHHHHHHHHHHC---------------CCccccc----------CCCCeeeeEEeeeecccccccCCCcccc
Q 017090 271 GDGDRLLHACQVIIDAFNEA---------------GLVFHRD----------YNKKLKLHATLMNIRHKKRRKGTRRVDY 325 (377)
Q Consensus 271 ~~~~~L~~l~~~l~~~f~~~---------------Gl~~~~~----------~~r~fkpHiTL~r~~~~~~~~~~~~~~~ 325 (377)
+....|+.|+..+...|... |+...++ --+.|..||||-..--... ..
T Consensus 51 ~~~~~L~~LAa~cV~~~d~fRAPls~aelaRR~~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l~~~~------~~- 123 (160)
T PF06299_consen 51 GPCPALQALAAACVRAFDPFRAPLSEAELARRRPAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRLDPAE------RA- 123 (160)
T ss_pred CCCHHHHHHHHHHHHhhhhccCCCChHHHhhcCcccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCCCHHH------HH-
Confidence 44588999999999888652 2221110 0267999999986431111 00
Q ss_pred ccHHHHHHH-hCCCccccEEecEEEEEee
Q 017090 326 FDARDIFKQ-FGSKEWGEYLIKEAHLSQR 353 (377)
Q Consensus 326 fda~~il~~-~~~~~fG~~~v~~I~Ls~~ 353 (377)
.+...++. |...--..+.|+.|.|+.-
T Consensus 124 -~~~~~l~~~f~~~l~~p~~id~laLf~e 151 (160)
T PF06299_consen 124 -RVEAALEAHFAPLLPEPLRIDSLALFGE 151 (160)
T ss_pred -HHHHHHHHHHHhhcCCCeeecceEEEec
Confidence 01223333 4444456789999999653
No 110
>PRK11538 ribosome-associated protein; Provisional
Probab=42.67 E-value=1.3e+02 Score=24.75 Aligned_cols=60 Identities=7% Similarity=0.141 Sum_probs=39.7
Q ss_pred HHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 017090 220 VNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 294 (377)
Q Consensus 220 v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~ 294 (377)
+..+.++|.+.+ ...-..+.+++...|-+ |.-+....+...++.+++.+.+.+.+.|+.+
T Consensus 7 ~~~i~~~l~dkK-------a~DI~vlDv~~~~~~~D--------y~VIatg~S~rh~~aia~~v~~~~k~~~~~~ 66 (105)
T PRK11538 7 QDFVIDKIDDLK-------GQDIIALDVQGKSSITD--------CMIICTGTSSRHVMSIADHVVQESRAAGLLP 66 (105)
T ss_pred HHHHHHHHHHcC-------CCCeEEEECCCCCcccC--------EEEEEEeCCHHHHHHHHHHHHHHHHHcCCCC
Confidence 444555555542 23456788899988876 3333332345789999999999998887754
No 111
>PRK15494 era GTPase Era; Provisional
Probab=40.03 E-value=19 Score=35.74 Aligned_cols=34 Identities=29% Similarity=0.389 Sum_probs=25.6
Q ss_pred EEEEeCcccc-ccccCCCchhHHH--------HHHHhCcEEEc
Q 017090 19 LDMQVGASVI-RFIKGKEGSTQKK--------FEKEMGVKIIL 52 (377)
Q Consensus 19 ~~i~Vp~~~~-~~iIG~~G~tik~--------ie~et~~~I~i 52 (377)
.+|.|+.+-+ +.|||+||++||+ ||+-+|++|..
T Consensus 275 ~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 275 QVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 5677777554 6789999999988 56667777766
No 112
>PRK00089 era GTPase Era; Reviewed
Probab=39.69 E-value=20 Score=34.42 Aligned_cols=34 Identities=35% Similarity=0.452 Sum_probs=24.6
Q ss_pred EEEEeCcccc-ccccCCCchhHHH--------HHHHhCcEEEc
Q 017090 19 LDMQVGASVI-RFIKGKEGSTQKK--------FEKEMGVKIIL 52 (377)
Q Consensus 19 ~~i~Vp~~~~-~~iIG~~G~tik~--------ie~et~~~I~i 52 (377)
.+|.|..+-+ +.|||+||++||+ ||+-+||+|..
T Consensus 228 ~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 228 ATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 3556665444 6789999999987 56667777776
No 113
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=39.14 E-value=11 Score=43.10 Aligned_cols=68 Identities=19% Similarity=0.070 Sum_probs=54.5
Q ss_pred eEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCC----CCcEEEEeCCHHHHHHHHHHHHHHHHhh
Q 017090 17 SVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKK----EDSIIIEGNSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 17 ~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~----~~~v~I~g~~~~~v~~A~~~I~~iv~~~ 85 (377)
..-.+.+|.--+..+||+||.+++.+..-||+-|.|..-.. +..+.+.|. .+.+..|..-|..++.++
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~-p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGR-PPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCC-ChhhhhhhccccceeecC
Confidence 35567788888999999999999999999999999987333 346777775 468888888888777654
No 114
>PF08302 tRNA_lig_CPD: Fungal tRNA ligase phosphodiesterase domain; InterPro: IPR015965 This entry represents a phosphodiesterase domain found in fungal tRNA ligases []. Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation
Probab=39.05 E-value=1.4e+02 Score=28.60 Aligned_cols=106 Identities=14% Similarity=0.079 Sum_probs=54.2
Q ss_pred CCcceEEeeccccCCHHHHHHHHHHHHHh-HHHhhhhc--------CCCCeEEEEccccCCCCCCCCceEEEEeeeccCC
Q 017090 202 PKTFHLTVLMLKLWNKDRVNAATNVLKSI-SSKVMDAL--------DNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGD 272 (377)
Q Consensus 202 p~~LHLTL~fLgl~~~~~v~~a~~~L~~i-~~~i~~~l--------~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~ 272 (377)
...||+||.-.....+..-+...+.+... ........ ....+.++|..|- |.+ ||+-+.|.-.+.
T Consensus 113 Q~~FHVTL~H~as~k~~~~k~lW~~y~~~~~~~~~~~~~~~~~~~~~~~~~~v~L~rlv-wd~-----rimai~V~~~~~ 186 (257)
T PF08302_consen 113 QPEFHVTLIHRASSKEQPAKELWKRYTKLYKSALKKNPKQEPTQTPTLGSCDVRLERLV-WDD-----RIMAIVVRIVPP 186 (257)
T ss_pred CCCCeEEEEecccCCcCcchHHHHHHHHHHHhhcccccccccccccccceEEEEEEEEE-ECC-----cEEEEEEEccCc
Confidence 35789999998776553311222222221 11111100 0135788888886 876 898887764321
Q ss_pred hhHHHHHHHHHHHHHHHCCCcccccCCCCeeeeEEeeeecccccccCCCccccccHHHHHHHhC
Q 017090 273 GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLHATLMNIRHKKRRKGTRRVDYFDARDIFKQFG 336 (377)
Q Consensus 273 ~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpHiTL~r~~~~~~~~~~~~~~~fda~~il~~~~ 336 (377)
...-. ...++.- -.=.|||||+-.... ..|+-...+++++.
T Consensus 187 ~~~~~----------~~~~~~c-----~N~~~HITVGT~~~~--------VkP~eSN~Ll~~~~ 227 (257)
T PF08302_consen 187 EDEED----------EVPEWEC-----TNKIPHITVGTRDPG--------VKPKESNDLLERWL 227 (257)
T ss_pred ccccc----------ccCCccc-----CCCCCEEEEEcCCCC--------CCcchHHHHHHHHH
Confidence 10000 0234432 224899999976321 22344445666554
No 115
>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=38.04 E-value=19 Score=34.33 Aligned_cols=30 Identities=23% Similarity=0.186 Sum_probs=22.8
Q ss_pred EEEEEeCcccc-ccccCCCchhHHHHHHHhC
Q 017090 18 VLDMQVGASVI-RFIKGKEGSTQKKFEKEMG 47 (377)
Q Consensus 18 ~~~i~Vp~~~~-~~iIG~~G~tik~ie~et~ 47 (377)
...|.|..+-+ +.|||++|++||+|..+..
T Consensus 222 ~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar 252 (270)
T TIGR00436 222 HALISVERESQKKIIIGKNGSMIKAIGIAAR 252 (270)
T ss_pred EEEEEECcCCceeEEEcCCcHHHHHHHHHHH
Confidence 34666776555 6788999999999987654
No 116
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=36.83 E-value=24 Score=37.24 Aligned_cols=35 Identities=23% Similarity=0.271 Sum_probs=29.3
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
+-.+-|-..+=|.+||++|+|.++|-++||-+-.|
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~i 134 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKI 134 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCccee
Confidence 34566777889999999999999999999966555
No 117
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=36.60 E-value=41 Score=34.90 Aligned_cols=28 Identities=25% Similarity=0.268 Sum_probs=24.5
Q ss_pred cccccccCCCchhHHHHHHHh-CcEEEcC
Q 017090 26 SVIRFIKGKEGSTQKKFEKEM-GVKIILP 53 (377)
Q Consensus 26 ~~~~~iIG~~G~tik~ie~et-~~~I~ip 53 (377)
+=+|..||++|..|+.|.++. |=+|+|=
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI 305 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVI 305 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEE
Confidence 559999999999999999998 7777763
No 118
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=36.50 E-value=33 Score=32.26 Aligned_cols=63 Identities=19% Similarity=0.237 Sum_probs=39.6
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCC-HHHHHHHHHHHHHHHHh
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNS-TDSVAKASEKIQAIIAE 84 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~-~~~v~~A~~~I~~iv~~ 84 (377)
-+++.||+-.+-.||||.|+-+..|=.=..-=+.. ++|.|.|.|-+ ...-.+...+..+|...
T Consensus 19 ~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~----d~G~i~i~g~~~~~~~s~~LAk~lSILkQ 82 (252)
T COG4604 19 DVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKK----DSGEITIDGLELTSTPSKELAKKLSILKQ 82 (252)
T ss_pred cceeeecCCceeEEECCCCccHHHHHHHHHHhccc----cCceEEEeeeecccCChHHHHHHHHHHHh
Confidence 56899999999999999998766654443322333 36889998831 11222334444455543
No 119
>COG5255 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.39 E-value=60 Score=30.27 Aligned_cols=34 Identities=18% Similarity=0.270 Sum_probs=24.6
Q ss_pred CCcceEEeecccc-CCHHHHHHHHHHHHHhHHHhh
Q 017090 202 PKTFHLTVLMLKL-WNKDRVNAATNVLKSISSKVM 235 (377)
Q Consensus 202 p~~LHLTL~fLgl-~~~~~v~~a~~~L~~i~~~i~ 235 (377)
.-.+||||++|.. +++++.++-..+|+++.+.+.
T Consensus 176 aY~FHITlgYl~~wltpee~a~~q~~l~e~~e~la 210 (239)
T COG5255 176 AYQFHITLGYLRIWLTPEEEAEWQAVLDELLEILA 210 (239)
T ss_pred ceEEEEEeeeEeeecChhhhHHHHHHHHHHHHHHH
Confidence 3579999999987 456666667777777755443
No 120
>PRK09256 hypothetical protein; Provisional
Probab=35.81 E-value=40 Score=29.38 Aligned_cols=54 Identities=26% Similarity=0.444 Sum_probs=37.6
Q ss_pred cCCCchhHHHHHHHhCcEEEc-------CC-------------CCCCCcEEEEe----CCHHHHHHHHHHHHHHHHhhhc
Q 017090 32 KGKEGSTQKKFEKEMGVKIIL-------PS-------------SKKEDSIIIEG----NSTDSVAKASEKIQAIIAEAVE 87 (377)
Q Consensus 32 IG~~G~tik~ie~et~~~I~i-------p~-------------~~~~~~v~I~g----~~~~~v~~A~~~I~~iv~~~~~ 87 (377)
=||||-+.++. +|.|+|.+ |. -..+|.++|++ ....+.+.|.+++..++.++..
T Consensus 23 SGPGGQ~VNKt--~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~~ 100 (138)
T PRK09256 23 SGPGGQNVNKV--STAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIREALK 100 (138)
T ss_pred CCCCccccccc--ceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHhh
Confidence 49999999885 45556553 31 01257788888 3456888999999999887543
No 121
>PF08975 2H-phosphodiest: Domain of unknown function (DUF1868); InterPro: IPR015069 This family consist of hypothetical bacterial proteins. ; PDB: 2FSQ_A.
Probab=34.79 E-value=42 Score=28.46 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=16.9
Q ss_pred eeEEEeccccchhhhccHHHHHHHHhcc
Q 017090 94 SHFVSLPLAVHPELVDKLVNFQNTILGI 121 (377)
Q Consensus 94 ~~fv~~Pl~~~p~I~~~~~~f~~~Il~~ 121 (377)
+.||| ++.........+...++.+.+.
T Consensus 14 NTvIc-hl~~~s~~~~al~~i~~~l~~~ 40 (118)
T PF08975_consen 14 NTVIC-HLPQDSPFYAALLAIQQRLRES 40 (118)
T ss_dssp EEEEE-EB-TTSHHHHHHHHHHHHHHTS
T ss_pred CeEEe-ecCCCChHHHHHHHHHHHHHhC
Confidence 45565 5555566777777777777654
No 122
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=33.09 E-value=40 Score=31.33 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=24.1
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEE
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKI 50 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I 50 (377)
..+.|-..+-|.+||++|+++++|.+.-.-..
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~ 73 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKKF 73 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHHh
Confidence 44445557789999999999999887765443
No 123
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=33.04 E-value=2.2e+02 Score=23.06 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=33.1
Q ss_pred CCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 017090 241 RPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 294 (377)
Q Consensus 241 ~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~ 294 (377)
.-..+.+++...+.+ |+-+....+...++.+++.+.+.+.+.|+.+
T Consensus 16 dI~vldv~~~~~~~d--------y~VI~Tg~S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 16 DIVVLDVRGKSSIAD--------YFVIASGTSSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred CEEEEECCCCCcccC--------EEEEEEeCCHHHHHHHHHHHHHHHHHcCCCc
Confidence 455677888887765 3333332345789999999999999888764
No 124
>COG1159 Era GTPase [General function prediction only]
Probab=32.66 E-value=26 Score=34.38 Aligned_cols=26 Identities=27% Similarity=0.299 Sum_probs=18.9
Q ss_pred EEEEeCccc-cccccCCCchhHHHHHH
Q 017090 19 LDMQVGASV-IRFIKGKEGSTQKKFEK 44 (377)
Q Consensus 19 ~~i~Vp~~~-~~~iIG~~G~tik~ie~ 44 (377)
..|.|+.+- =+.|||++|+++|+|-.
T Consensus 231 a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 231 ATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEecCCccceEECCCcHHHHHHHH
Confidence 356676644 46789999999998643
No 125
>CHL00048 rps3 ribosomal protein S3
Probab=32.33 E-value=42 Score=31.39 Aligned_cols=32 Identities=3% Similarity=0.220 Sum_probs=24.3
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcE
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVK 49 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~ 49 (377)
...+.|=..+-+.|||++|+++++|.+.-.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k~ 98 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQKE 98 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHHHH
Confidence 35555666778999999999999988776433
No 126
>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=32.15 E-value=81 Score=30.29 Aligned_cols=48 Identities=13% Similarity=0.258 Sum_probs=37.1
Q ss_pred ceEEEEEeCccccccccCCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeCC
Q 017090 16 LSVLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGNS 67 (377)
Q Consensus 16 ~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~~ 67 (377)
..-+.+.|++-.+-.|||+.|+=+..|-.--+--+++. +|.|.+.|.+
T Consensus 20 L~~Vnl~I~~GE~VaiIG~SGaGKSTLLR~lngl~d~t----~G~i~~~g~~ 67 (258)
T COG3638 20 LKDVNLEINQGEMVAIIGPSGAGKSTLLRSLNGLVDPT----SGEILFNGVQ 67 (258)
T ss_pred eeeEeEEeCCCcEEEEECCCCCcHHHHHHHHhcccCCC----cceEEecccc
Confidence 34778999999999999999998887777665444432 6888888853
No 127
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=32.13 E-value=2.5e+02 Score=27.35 Aligned_cols=83 Identities=14% Similarity=0.213 Sum_probs=48.8
Q ss_pred cceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceE-EEEeeeccCChhHHHHHHHH
Q 017090 204 TFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARI-LYAPVEEIGDGDRLLHACQV 282 (377)
Q Consensus 204 ~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rV-Lya~v~~~~~~~~L~~l~~~ 282 (377)
..++++++=. +.++++|.+.|.++.......+..++..+.+.+++-..= ...| .|+... +-...-.++...
T Consensus 185 r~~~~v~V~y---~~d~~~~~~il~~~~~~~~~vl~~p~p~v~~~~~~dssi---~~~v~~wv~~~--~~~~~~~~~~~~ 256 (286)
T PRK10334 185 RNEFIIGVAY---DSDIDQVKQILTNIIQSEDRILKDREMTVRLNELGASSI---NFVVRVWSNSG--DLQNVYWDVLER 256 (286)
T ss_pred EEEEEEEecC---CCCHHHHHHHHHHHHHhCCceecCCCCEEEEEeeeCceE---EEEEEEEEecc--hhHHHHHHHHHH
Confidence 4667766544 345667777777765544445555566676665443221 1122 344432 222334567788
Q ss_pred HHHHHHHCCCcc
Q 017090 283 IIDAFNEAGLVF 294 (377)
Q Consensus 283 l~~~f~~~Gl~~ 294 (377)
+.++|.++|+..
T Consensus 257 I~~~f~~~gI~i 268 (286)
T PRK10334 257 IKREFDAAGISF 268 (286)
T ss_pred HHHHHHHCCCcC
Confidence 999999999987
No 128
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=30.81 E-value=70 Score=26.63 Aligned_cols=47 Identities=21% Similarity=0.297 Sum_probs=34.7
Q ss_pred CCCchhHHHHHHHhCcEEEcCCCCCCCcEEEEeC----CHHHHHHHHHHHHHHHHhh
Q 017090 33 GKEGSTQKKFEKEMGVKIILPSSKKEDSIIIEGN----STDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 33 G~~G~tik~ie~et~~~I~ip~~~~~~~v~I~g~----~~~~v~~A~~~I~~iv~~~ 85 (377)
||||-.+++- +|.|+|...+ +| |+|.+. ...+.+.|.+++...+.++
T Consensus 23 GpGGQ~VNk~--~s~V~l~h~p---tg-i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~ 73 (113)
T PF00472_consen 23 GPGGQNVNKT--NSKVRLRHIP---TG-IVVKCQESRSQHQNREDALEKLREKLDEA 73 (113)
T ss_dssp SSSSCHHHSS--SEEEEEEETT---TT-EEEEEESSSSHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCccccc--CCEEEEEEec---cc-EEEEEcccCCHHHHHHHHHHHHHHHHHHH
Confidence 9999988764 5667777764 34 666662 4568889999998888764
No 129
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=30.77 E-value=1.5e+02 Score=27.00 Aligned_cols=47 Identities=11% Similarity=0.064 Sum_probs=37.5
Q ss_pred CchhHHHHHHHhCcEEEcCCCCCCCcEEEEe----CCHHHHHHHHHHHHHHHH
Q 017090 35 EGSTQKKFEKEMGVKIILPSSKKEDSIIIEG----NSTDSVAKASEKIQAIIA 83 (377)
Q Consensus 35 ~G~tik~ie~et~~~I~ip~~~~~~~v~I~g----~~~~~v~~A~~~I~~iv~ 83 (377)
....++.|++.|+|-|..... .+.+.|++ .+...++.|++-+...+.
T Consensus 114 ~~~~l~~i~~~t~~~ie~~~~--~~~~~i~~~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 114 TPDLLEEIQKLTNVYIEKNPD--GNKLKISWLASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred cHHHHHHHHHHHcEEEEECCC--CCeEEEEEEeeccccchHHHHHHHHHHhcc
Confidence 477899999999999998762 34677777 677889999998887764
No 130
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=30.74 E-value=56 Score=29.31 Aligned_cols=55 Identities=22% Similarity=0.364 Sum_probs=39.6
Q ss_pred ccCCCchhHHHHHHHhCcEEEcCCCCC---------------------CCcEEEEeC----CHHHHHHHHHHHHHHHHhh
Q 017090 31 IKGKEGSTQKKFEKEMGVKIILPSSKK---------------------EDSIIIEGN----STDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 31 iIG~~G~tik~ie~et~~~I~ip~~~~---------------------~~~v~I~g~----~~~~v~~A~~~I~~iv~~~ 85 (377)
==||||.+.+++- |.|.+.++-... .|.++|.+. ...+++.|.++|..++..+
T Consensus 49 SSGPGGQNVNKvN--TKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~~I~~~ 126 (172)
T KOG3429|consen 49 SSGPGGQNVNKVN--TKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAA 126 (172)
T ss_pred cCCCCCccccccc--ceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHHHHHHH
Confidence 3499999999874 555555553321 478999883 3457899999999999886
Q ss_pred hc
Q 017090 86 VE 87 (377)
Q Consensus 86 ~~ 87 (377)
..
T Consensus 127 ~~ 128 (172)
T KOG3429|consen 127 EQ 128 (172)
T ss_pred hc
Confidence 65
No 131
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=29.62 E-value=2.5e+02 Score=23.89 Aligned_cols=56 Identities=16% Similarity=0.274 Sum_probs=35.8
Q ss_pred CHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCCCCCCCceEEEEeeeccCChhHHHHHHHHHHHHHH
Q 017090 216 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMRGSKDKARILYAPVEEIGDGDRLLHACQVIIDAFN 288 (377)
Q Consensus 216 ~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~~dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~ 288 (377)
.++|++....+|++ ..+.++-=-=..+. ++||+.|+-+...++ -..||..++++|.
T Consensus 66 l~~EV~pvi~aL~~-----------~GI~vtAlHNH~l~---e~Prl~ymH~~~~gd---p~~lA~~vr~Ald 121 (123)
T PF07485_consen 66 LEDEVNPVISALRK-----------NGIEVTALHNHWLF---EQPRLFYMHIWGVGD---PAKLARKVRAALD 121 (123)
T ss_pred cHHHHHHHHHHHHH-----------CCceEEEEeccccc---CCCCEEEEEEEecCC---HHHHHHHHHHHHh
Confidence 37899988887765 23333322223333 357999999987543 4456888887764
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=29.22 E-value=43 Score=36.41 Aligned_cols=36 Identities=22% Similarity=0.243 Sum_probs=30.6
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCcEEEcC
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIILP 53 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~ip 53 (377)
+-.+-|-..+=|.+||++|.|+++|-++||-+-.|-
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~ 129 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVV 129 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEE
Confidence 346667778899999999999999999999876663
No 133
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=28.55 E-value=1.9e+02 Score=24.79 Aligned_cols=36 Identities=17% Similarity=0.413 Sum_probs=27.8
Q ss_pred CCCCceEEEEeeeccCChhHHHHHHHHHHHHHHHCCCcc
Q 017090 256 SKDKARILYAPVEEIGDGDRLLHACQVIIDAFNEAGLVF 294 (377)
Q Consensus 256 dp~~~rVLya~v~~~~~~~~L~~l~~~l~~~f~~~Gl~~ 294 (377)
+|++++++|+...+ -++..+..+...+.+.+.|-.+
T Consensus 93 e~eRv~~~wiSa~E---~ekf~e~~~efv~~i~~lGpnp 128 (132)
T COG1908 93 EPERVRVLWISAAE---GEKFAETINEFVERIKELGPNP 128 (132)
T ss_pred CcceEEEEEEehhh---HHHHHHHHHHHHHHHHHhCCCc
Confidence 47888999999876 3678777888888888877544
No 134
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=28.00 E-value=63 Score=25.15 Aligned_cols=35 Identities=23% Similarity=0.421 Sum_probs=21.3
Q ss_pred CHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCC
Q 017090 216 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 254 (377)
Q Consensus 216 ~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~ 254 (377)
+..++..+.++|-+. +.+.|.... .+.|.|+|+|.
T Consensus 17 ~~~~v~~vl~~l~~~---i~~~L~~g~-~V~i~g~G~F~ 51 (90)
T smart00411 17 SKKDAKAAVDAFLEI---ITEALKKGE-KVELRGFGTFE 51 (90)
T ss_pred CHHHHHHHHHHHHHH---HHHHHhCCC-eEEEeCcEEEE
Confidence 456666555555443 444443222 78899999994
No 135
>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=27.74 E-value=58 Score=30.07 Aligned_cols=31 Identities=10% Similarity=0.159 Sum_probs=23.5
Q ss_pred EEEEEeCccccccccCCCchhHHHHHHHhCc
Q 017090 18 VLDMQVGASVIRFIKGKEGSTQKKFEKEMGV 48 (377)
Q Consensus 18 ~~~i~Vp~~~~~~iIG~~G~tik~ie~et~~ 48 (377)
...+.|-...-|.+||++|+.+++|.++-.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 3555566666799999999999998776543
No 136
>PLN00062 TATA-box-binding protein; Provisional
Probab=27.19 E-value=1e+02 Score=27.96 Aligned_cols=30 Identities=23% Similarity=0.379 Sum_probs=25.9
Q ss_pred CCcEEEEeC-CHHHHHHHHHHHHHHHHhhhc
Q 017090 58 EDSIIIEGN-STDSVAKASEKIQAIIAEAVE 87 (377)
Q Consensus 58 ~~~v~I~g~-~~~~v~~A~~~I~~iv~~~~~ 87 (377)
+|.|+|+|. +.+.+.+|.+.|..++.+.++
T Consensus 146 sGkvvitGaks~~~~~~ai~~i~p~L~~~~~ 176 (179)
T PLN00062 146 SGKIVITGAKVREEIYTAFENIYPVLTEFRK 176 (179)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHHHhcc
Confidence 799999994 788999999999999987553
No 137
>PRK15245 type III effector phosphothreonine lyase; Provisional
Probab=26.46 E-value=4.4e+02 Score=24.78 Aligned_cols=92 Identities=13% Similarity=0.255 Sum_probs=53.5
Q ss_pred CCcceEEeeccccCCHHHHHHHHHHHHHhHHHhhhhcCCCCe-EEEEccccCCCCCCCCc-----eEEEEeeeccCC---
Q 017090 202 PKTFHLTVLMLKLWNKDRVNAATNVLKSISSKVMDALDNRPL-FIRLKGLDLMRGSKDKA-----RILYAPVEEIGD--- 272 (377)
Q Consensus 202 p~~LHLTL~fLgl~~~~~v~~a~~~L~~i~~~i~~~l~~~p~-~l~l~Gl~~F~~dp~~~-----rVLya~v~~~~~--- 272 (377)
-+++||.+ ..+++..|.++|..+--. ...|+ +-.+..+..-.. -+++ =.||+++...+.
T Consensus 102 GDK~HiSV------~~~qv~qAF~als~lLfS-----eDSPiDKWKVTDM~rv~q-qsRV~~GAQfTLYvKpd~edsqYs 169 (241)
T PRK15245 102 GDKFHISV------ARDQVPQAFQALSGLLFS-----EDSPVDKWKVTDMERVSQ-QSRVGLGAQFTLYVKPDQENSQYS 169 (241)
T ss_pred CceEEEEe------cHHHHHHHHHHhhhhhcC-----CCCCcceeeeccccccCc-cchhcccceEEEEecCccccccCC
Confidence 37899876 468899999998876311 22333 222223222211 1111 239999876542
Q ss_pred ---hhHHHHHHHHHHHHHHHCCCcccccCCCCeeee
Q 017090 273 ---GDRLLHACQVIIDAFNEAGLVFHRDYNKKLKLH 305 (377)
Q Consensus 273 ---~~~L~~l~~~l~~~f~~~Gl~~~~~~~r~fkpH 305 (377)
..+...+...|+..|.++|+.+.+.....+.||
T Consensus 170 a~~l~k~r~Fie~lE~~L~~~gi~pG~~P~SDV~pe 205 (241)
T PRK15245 170 ASFLHKTRQFIECLESRLSENGVISGQCPESDVHPE 205 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCCCCCccccCcc
Confidence 234556778889999999998743222334444
No 138
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=26.46 E-value=78 Score=24.39 Aligned_cols=35 Identities=20% Similarity=0.310 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHHHHhHHHhhhhcCCCCeEEEEccccCCC
Q 017090 216 NKDRVNAATNVLKSISSKVMDALDNRPLFIRLKGLDLMR 254 (377)
Q Consensus 216 ~~~~v~~a~~~L~~i~~~i~~~l~~~p~~l~l~Gl~~F~ 254 (377)
+..++..+.+.|-+ .+.+.|... -.+.|.|+|.|.
T Consensus 16 ~~~~v~~vl~~~~~---~i~~~L~~g-~~V~l~~~G~F~ 50 (87)
T cd00591 16 SKKDAEAAVDAFLD---VITEALAKG-EKVELPGFGTFE 50 (87)
T ss_pred CHHHHHHHHHHHHH---HHHHHHhCC-CeEEEeCCEEEE
Confidence 45555555554444 344444322 278889999994
No 139
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=26.01 E-value=1.8e+02 Score=27.44 Aligned_cols=34 Identities=12% Similarity=0.239 Sum_probs=25.5
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhCcEEEc
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMGVKIIL 52 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~~~I~i 52 (377)
..+.|-..+-|.|||++|..+++|.++-.-.+.+
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~ 79 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRFGF 79 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHhCC
Confidence 5555556667999999999999988776655443
No 140
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=25.56 E-value=58 Score=32.52 Aligned_cols=30 Identities=10% Similarity=0.228 Sum_probs=23.9
Q ss_pred EEEEEeCcccc-ccccCCCchhHHHHHHHhC
Q 017090 18 VLDMQVGASVI-RFIKGKEGSTQKKFEKEMG 47 (377)
Q Consensus 18 ~~~i~Vp~~~~-~~iIG~~G~tik~ie~et~ 47 (377)
...+.+|+... ..|||+||..|++|-++.+
T Consensus 329 ~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 329 QVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 55777887655 5689999999999987765
No 141
>COG0097 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]
Probab=25.09 E-value=1.1e+02 Score=27.92 Aligned_cols=34 Identities=24% Similarity=0.477 Sum_probs=27.0
Q ss_pred hCcEEEcCCCCCCCcEEEEeCCHHHHHHHHHHHHHHH
Q 017090 46 MGVKIILPSSKKEDSIIIEGNSTDSVAKASEKIQAII 82 (377)
Q Consensus 46 t~~~I~ip~~~~~~~v~I~g~~~~~v~~A~~~I~~iv 82 (377)
.|+++.+|. ..+|+|+|.|++.|-+-.+.|++.-
T Consensus 119 ~gi~v~v~~---~t~I~v~GidKe~VGQ~AA~Ir~~r 152 (178)
T COG0097 119 EGITVEVPG---PTEIVVEGIDKELVGQVAANIRAAR 152 (178)
T ss_pred CCeEEEecC---CCEEEEEcCCHHHHhHHHHHHHhcc
Confidence 456666665 4679999999999999998888654
No 142
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=25.02 E-value=1.1e+02 Score=27.50 Aligned_cols=37 Identities=16% Similarity=0.216 Sum_probs=29.3
Q ss_pred hCcEEEcCCCCCCCcEEEEeC-CHHHHHHHHHHHHHHHHhh
Q 017090 46 MGVKIILPSSKKEDSIIIEGN-STDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 46 t~~~I~ip~~~~~~~v~I~g~-~~~~v~~A~~~I~~iv~~~ 85 (377)
.+|.+.|=+ +|.++|||. +.+.+..|.+++..++.+.
T Consensus 46 Pk~t~lIF~---sGKiviTGaks~~~~~~a~~~~~~~l~~~ 83 (174)
T cd04517 46 PRATASVWS---SGKITITGATSEEEAKQAARRAARLLQKL 83 (174)
T ss_pred CcEEEEEEC---CCeEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 456666655 799999995 8889999988888877664
No 143
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=24.89 E-value=1.4e+02 Score=26.97 Aligned_cols=38 Identities=24% Similarity=0.289 Sum_probs=29.9
Q ss_pred HhCcEEEcCCCCCCCcEEEEe-CCHHHHHHHHHHHHHHHHhh
Q 017090 45 EMGVKIILPSSKKEDSIIIEG-NSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 45 et~~~I~ip~~~~~~~v~I~g-~~~~~v~~A~~~I~~iv~~~ 85 (377)
+-+|.+.|=+ +|.++||| .|.+.+..|.++|..++.+.
T Consensus 45 ~Pk~t~lIF~---SGKiviTGaks~e~a~~a~~~i~~~L~~~ 83 (174)
T cd04516 45 EPKTTALIFS---SGKMVCTGAKSEDDSKLAARKYARIIQKL 83 (174)
T ss_pred CCcEEEEEEC---CCeEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 4466666655 79999999 68888999999998888663
No 144
>PRK00394 transcription factor; Reviewed
Probab=24.14 E-value=1.2e+02 Score=27.46 Aligned_cols=27 Identities=33% Similarity=0.495 Sum_probs=23.3
Q ss_pred CCcEEEEeC-CHHHHHHHHHHHHHHHHh
Q 017090 58 EDSIIIEGN-STDSVAKASEKIQAIIAE 84 (377)
Q Consensus 58 ~~~v~I~g~-~~~~v~~A~~~I~~iv~~ 84 (377)
+|.|+|+|. +.+.+.+|.+.|..++.+
T Consensus 147 SGKvvitGaks~~~~~~a~~~i~~~l~~ 174 (179)
T PRK00394 147 SGKLVITGAKSEEDAEKAVEKILEKLEE 174 (179)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHHH
Confidence 799999994 888899999999887765
No 145
>PRK15031 5-carboxymethyl-2-hydroxymuconate delta-isomerase; Provisional
Probab=23.69 E-value=1.9e+02 Score=24.79 Aligned_cols=45 Identities=13% Similarity=0.161 Sum_probs=28.7
Q ss_pred CcceEEeeccccCCHHHHHHHHHHHHH-hHHHhhhhcCCCCeEEEE
Q 017090 203 KTFHLTVLMLKLWNKDRVNAATNVLKS-ISSKVMDALDNRPLFIRL 247 (377)
Q Consensus 203 ~~LHLTL~fLgl~~~~~v~~a~~~L~~-i~~~i~~~l~~~p~~l~l 247 (377)
.=.|+||.++.=-++++.+.+.+.|-. ++..+.+.+....+.|++
T Consensus 60 ~Fihv~l~i~~GRs~e~k~~l~~~l~~~l~~~~~~~~~~~~~~LS~ 105 (126)
T PRK15031 60 AFVHMTLKIGAGRSLESRQEVGEMLFALIKAHFAALMESRYLALSF 105 (126)
T ss_pred cEEEEEeeecCCCCHHHHHHHHHHHHHHHHHHhhhhhcccceEEEE
Confidence 346999999988888888877775544 444444444433344433
No 146
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=23.19 E-value=1.5e+02 Score=26.75 Aligned_cols=26 Identities=35% Similarity=0.542 Sum_probs=22.1
Q ss_pred CCcEEEEeC-CHHHHHHHHHHHHHHHH
Q 017090 58 EDSIIIEGN-STDSVAKASEKIQAIIA 83 (377)
Q Consensus 58 ~~~v~I~g~-~~~~v~~A~~~I~~iv~ 83 (377)
+|.|+|+|. +.+.+.+|.+.|..++.
T Consensus 147 sGkvvitGaks~~~~~~a~~~i~~~L~ 173 (174)
T cd00652 147 SGKIVITGAKSREDIYEAVEKIYPILK 173 (174)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 799999994 77889999999887764
No 147
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=23.16 E-value=1.5e+02 Score=26.79 Aligned_cols=26 Identities=35% Similarity=0.501 Sum_probs=22.4
Q ss_pred CCcEEEEe-CCHHHHHHHHHHHHHHHH
Q 017090 58 EDSIIIEG-NSTDSVAKASEKIQAIIA 83 (377)
Q Consensus 58 ~~~v~I~g-~~~~~v~~A~~~I~~iv~ 83 (377)
+|.|+|+| .+.+.+.+|.+.|..++.
T Consensus 147 sGkivitGaks~~~~~~a~~~i~pil~ 173 (174)
T cd04517 147 TGSVTVTGARSMEDVREAVEKIYPIVF 173 (174)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 79999999 577999999999987764
No 148
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=22.39 E-value=1.6e+02 Score=26.41 Aligned_cols=36 Identities=19% Similarity=0.322 Sum_probs=28.7
Q ss_pred CcEEEcCCCCCCCcEEEEe-CCHHHHHHHHHHHHHHHHhh
Q 017090 47 GVKIILPSSKKEDSIIIEG-NSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 47 ~~~I~ip~~~~~~~v~I~g-~~~~~v~~A~~~I~~iv~~~ 85 (377)
++.+.|=+ +|.|+|+| .|.+.+..|.+++..++.+.
T Consensus 47 ~~t~lIf~---sGKivitGaks~~~~~~a~~~~~~~L~~~ 83 (174)
T cd00652 47 KTTALIFS---SGKMVITGAKSEEDAKLAARKYARILQKL 83 (174)
T ss_pred cEEEEEEC---CCEEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 56666654 79999999 58889999999888887654
No 149
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=22.29 E-value=1.2e+02 Score=27.27 Aligned_cols=27 Identities=26% Similarity=0.466 Sum_probs=23.1
Q ss_pred CCcEEEEeC-CHHHHHHHHHHHHHHHHh
Q 017090 58 EDSIIIEGN-STDSVAKASEKIQAIIAE 84 (377)
Q Consensus 58 ~~~v~I~g~-~~~~v~~A~~~I~~iv~~ 84 (377)
+|.|+|+|. +.+.+.+|.+.|..++.+
T Consensus 146 sGkvvitGaks~~~~~~a~~~i~p~L~~ 173 (174)
T cd04516 146 SGKIVLTGAKSREEIYQAFENIYPILLQ 173 (174)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 699999995 888899999999887654
No 150
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=21.18 E-value=2e+02 Score=25.87 Aligned_cols=45 Identities=18% Similarity=0.266 Sum_probs=27.8
Q ss_pred CCCcEEEEeCCHHHHHHHHHHHHHHHHhhhcCCCCCceeEEEecc
Q 017090 57 KEDSIIIEGNSTDSVAKASEKIQAIIAEAVESPSLDYSHFVSLPL 101 (377)
Q Consensus 57 ~~~~v~I~g~~~~~v~~A~~~I~~iv~~~~~~~~~~~~~fv~~Pl 101 (377)
++..+.+.|.+.+.+..|..++..+--.......-.--+.+.||+
T Consensus 64 DshniiviG~~~~dm~~A~n~l~~~gGG~vvv~~g~v~a~lpLpi 108 (171)
T PF13382_consen 64 DSHNIIVIGTNDEDMALAANRLIEMGGGIVVVDDGEVLAELPLPI 108 (171)
T ss_dssp TT--EEEEESSHHHHHHHHHHHHHTTSEEEEEETTEEEEEEE-TB
T ss_pred CCCCEEEEECCHHHHHHHHHHHHHhCCCEEEEECCEEEEEEeccc
Confidence 357789999999999999999987653322210112356666665
No 151
>PLN00062 TATA-box-binding protein; Provisional
Probab=21.06 E-value=1.8e+02 Score=26.32 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=28.9
Q ss_pred HhCcEEEcCCCCCCCcEEEEe-CCHHHHHHHHHHHHHHHHhh
Q 017090 45 EMGVKIILPSSKKEDSIIIEG-NSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 45 et~~~I~ip~~~~~~~v~I~g-~~~~~v~~A~~~I~~iv~~~ 85 (377)
+-++.+.|=+ +|.|+||| .|.+.+..|.+++..++.+.
T Consensus 45 ~Pk~t~lIF~---SGKiviTGaks~e~a~~a~~~~~~~L~~l 83 (179)
T PLN00062 45 EPKTTALIFA---SGKMVCTGAKSEHDSKLAARKYARIIQKL 83 (179)
T ss_pred CCcEEEEEEC---CCeEEEEecCCHHHHHHHHHHHHHHHHHc
Confidence 3345666654 79999999 58888999999888887653
No 152
>PTZ00179 60S ribosomal protein L9; Provisional
Probab=20.80 E-value=1.9e+02 Score=26.53 Aligned_cols=38 Identities=21% Similarity=0.411 Sum_probs=29.3
Q ss_pred hCcEEEcCCC-CCCCcEEEEeCCHHHHHHHHHHHHHHHH
Q 017090 46 MGVKIILPSS-KKEDSIIIEGNSTDSVAKASEKIQAIIA 83 (377)
Q Consensus 46 t~~~I~ip~~-~~~~~v~I~g~~~~~v~~A~~~I~~iv~ 83 (377)
.|++|.+|.+ ...+.|+|+|.+.+.|-+-...|+....
T Consensus 126 ~gv~v~~~~~~~~k~~i~i~G~DKq~Vgq~AA~i~~~~~ 164 (189)
T PTZ00179 126 DTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCL 164 (189)
T ss_pred CCEEEEecCCcccCCEEEEEeCCHHHHHHHHHHHHHhhc
Confidence 3566666653 2236799999999999999999998764
No 153
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=20.73 E-value=2.4e+02 Score=26.66 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=25.2
Q ss_pred eccccceEEEEEeCccccccccCCCchhHHHHHHHhC
Q 017090 11 IDLISLSVLDMQVGASVIRFIKGKEGSTQKKFEKEMG 47 (377)
Q Consensus 11 ~~~~~~~~~~i~Vp~~~~~~iIG~~G~tik~ie~et~ 47 (377)
|-|.. ....|.|=...-+.|||++|+.+++|.+.-.
T Consensus 57 I~R~~-~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 57 IERPA-KRVRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred EEEcC-CeEEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 44532 2355555556679999999999999877654
No 154
>PRK00394 transcription factor; Reviewed
Probab=20.54 E-value=1.8e+02 Score=26.33 Aligned_cols=36 Identities=14% Similarity=0.258 Sum_probs=28.3
Q ss_pred CcEEEcCCCCCCCcEEEEe-CCHHHHHHHHHHHHHHHHhh
Q 017090 47 GVKIILPSSKKEDSIIIEG-NSTDSVAKASEKIQAIIAEA 85 (377)
Q Consensus 47 ~~~I~ip~~~~~~~v~I~g-~~~~~v~~A~~~I~~iv~~~ 85 (377)
+|.+.|=+ +|.++|+| .|.+.+..|.+++..++...
T Consensus 46 k~t~lIf~---sGKiv~tGa~S~~~a~~a~~~~~~~l~~~ 82 (179)
T PRK00394 46 KIAALIFR---SGKVVCTGAKSVEDLHEAVKIIIKKLKEL 82 (179)
T ss_pred ceEEEEEc---CCcEEEEccCCHHHHHHHHHHHHHHHHHc
Confidence 36666655 79999999 68888888888888777653
No 155
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=20.53 E-value=1.6e+02 Score=26.55 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=22.1
Q ss_pred CCcEEEEe-CCHHHHHHHHHHHHHHHHh
Q 017090 58 EDSIIIEG-NSTDSVAKASEKIQAIIAE 84 (377)
Q Consensus 58 ~~~v~I~g-~~~~~v~~A~~~I~~iv~~ 84 (377)
+|.|+||| .+.+.+.+|.+.|..++.+
T Consensus 146 SGKvvitGaks~~~~~~a~~~i~~~l~~ 173 (174)
T cd04518 146 SGKMVITGAKSEEDAKRAVEKLLSRLKE 173 (174)
T ss_pred CCEEEEEecCCHHHHHHHHHHHHHHHhh
Confidence 79999999 5888888888888776643
No 156
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=20.36 E-value=95 Score=28.94 Aligned_cols=29 Identities=21% Similarity=0.417 Sum_probs=22.7
Q ss_pred EEEEeCccccccccCCCchhHHHHHHHhC
Q 017090 19 LDMQVGASVIRFIKGKEGSTQKKFEKEMG 47 (377)
Q Consensus 19 ~~i~Vp~~~~~~iIG~~G~tik~ie~et~ 47 (377)
..|.|-..+-+.|||++|+.+++|.+.-.
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~ 92 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQ 92 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHH
Confidence 45666666679999999999999876654
Done!