Query 020173
Match_columns 330
No_of_seqs 163 out of 1689
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 07:37:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020173.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020173hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2192 PolyC-binding hnRNP-K 100.0 1E-38 2.2E-43 274.3 21.9 276 16-321 20-384 (390)
2 KOG2193 IGF-II mRNA-binding pr 100.0 2.8E-36 6E-41 273.5 18.5 267 38-321 187-481 (584)
3 KOG1676 K-homology type RNA bi 100.0 1.5E-34 3.2E-39 273.9 23.8 254 46-325 50-304 (600)
4 KOG1676 K-homology type RNA bi 100.0 2.4E-34 5.3E-39 272.4 20.9 249 47-321 136-389 (600)
5 KOG2191 RNA-binding protein NO 100.0 2.2E-31 4.8E-36 235.2 22.1 295 17-323 5-317 (402)
6 KOG2190 PolyC-binding proteins 100.0 2.1E-30 4.5E-35 249.0 26.6 265 48-320 41-408 (485)
7 KOG2193 IGF-II mRNA-binding pr 100.0 7.8E-31 1.7E-35 238.1 13.9 245 47-323 277-566 (584)
8 KOG2191 RNA-binding protein NO 99.9 3.8E-24 8.2E-29 189.5 16.6 168 141-325 37-208 (402)
9 KOG2190 PolyC-binding proteins 99.8 8.5E-19 1.8E-23 169.0 17.0 157 143-322 43-209 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.7 3.4E-17 7.5E-22 141.6 11.0 150 142-325 47-197 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.7 8.7E-17 1.9E-21 136.1 12.7 138 147-321 2-151 (172)
12 PRK13763 putative RNA-processi 99.7 1.3E-15 2.7E-20 129.9 14.6 141 144-321 4-157 (180)
13 TIGR03665 arCOG04150 arCOG0415 99.6 1.3E-15 2.9E-20 128.9 11.0 140 54-222 2-154 (172)
14 PRK13763 putative RNA-processi 99.6 1.1E-14 2.3E-19 124.2 12.7 147 50-221 3-159 (180)
15 cd02396 PCBP_like_KH K homolog 99.5 4.6E-14 1E-18 100.1 7.2 63 253-315 1-64 (65)
16 KOG2279 Kinase anchor protein 99.4 1E-12 2.3E-17 124.4 11.3 243 47-317 65-364 (608)
17 PF00013 KH_1: KH domain syndr 99.4 4.9E-13 1.1E-17 93.3 6.3 60 253-315 1-60 (60)
18 cd02396 PCBP_like_KH K homolog 99.4 5.7E-13 1.2E-17 94.5 5.5 63 51-118 1-64 (65)
19 cd02394 vigilin_like_KH K homo 99.4 7.6E-13 1.6E-17 93.0 5.7 61 254-316 2-62 (62)
20 cd00105 KH-I K homology RNA-bi 99.3 4.1E-12 9E-17 89.6 7.3 62 254-315 2-63 (64)
21 cd02393 PNPase_KH Polynucleoti 99.3 5.8E-12 1.2E-16 88.0 6.9 59 252-316 2-61 (61)
22 cd02394 vigilin_like_KH K homo 99.1 1E-10 2.2E-15 82.0 6.2 60 145-213 2-61 (62)
23 cd00105 KH-I K homology RNA-bi 99.1 1.4E-10 2.9E-15 81.8 6.1 62 52-118 2-63 (64)
24 PF00013 KH_1: KH domain syndr 99.1 1.4E-10 3E-15 80.8 5.9 60 144-213 1-60 (60)
25 KOG2208 Vigilin [Lipid transpo 99.1 8.7E-10 1.9E-14 112.6 13.5 229 50-318 201-485 (753)
26 PF13014 KH_3: KH domain 99.1 2.7E-10 5.8E-15 73.7 5.1 42 262-303 1-43 (43)
27 COG1094 Predicted RNA-binding 99.0 3.3E-09 7.2E-14 89.3 11.8 151 49-223 7-168 (194)
28 smart00322 KH K homology RNA-b 99.0 1.9E-09 4.1E-14 76.4 8.8 66 252-319 3-68 (69)
29 cd02393 PNPase_KH Polynucleoti 99.0 1.3E-09 2.8E-14 76.0 7.7 57 144-213 3-60 (61)
30 PF13014 KH_3: KH domain 99.0 3.3E-10 7.2E-15 73.3 4.4 42 60-101 1-43 (43)
31 COG1094 Predicted RNA-binding 98.9 4.9E-08 1.1E-12 82.4 12.7 141 144-321 9-164 (194)
32 KOG2279 Kinase anchor protein 98.8 1.9E-09 4.1E-14 102.5 3.9 146 141-323 66-211 (608)
33 KOG2208 Vigilin [Lipid transpo 98.8 1.8E-08 3.8E-13 103.1 8.5 218 48-322 345-563 (753)
34 smart00322 KH K homology RNA-b 98.7 8.6E-08 1.9E-12 67.7 8.9 66 143-217 3-68 (69)
35 KOG2113 Predicted RNA binding 98.6 8.4E-08 1.8E-12 85.5 5.8 154 141-317 24-179 (394)
36 cd02395 SF1_like-KH Splicing f 98.6 2E-07 4.3E-12 73.9 7.1 60 261-320 15-94 (120)
37 KOG2113 Predicted RNA binding 98.4 2.5E-07 5.5E-12 82.5 5.2 151 48-216 24-180 (394)
38 cd02395 SF1_like-KH Splicing f 98.4 6.3E-07 1.4E-11 71.0 6.5 71 53-125 3-96 (120)
39 TIGR02696 pppGpp_PNP guanosine 98.2 9.7E-06 2.1E-10 81.9 10.5 63 252-320 578-641 (719)
40 PRK08406 transcription elongat 98.0 2.5E-05 5.5E-10 63.7 8.0 103 50-178 32-134 (140)
41 PRK08406 transcription elongat 98.0 1.9E-05 4.1E-10 64.4 6.6 103 144-288 33-135 (140)
42 TIGR03591 polynuc_phos polyrib 97.8 6.2E-05 1.3E-09 77.0 8.8 63 252-320 551-614 (684)
43 KOG0119 Splicing factor 1/bran 97.7 0.00039 8.5E-09 66.2 10.5 72 251-322 137-231 (554)
44 TIGR01952 nusA_arch NusA famil 97.6 0.00038 8.3E-09 56.7 8.2 103 51-179 34-136 (141)
45 TIGR02696 pppGpp_PNP guanosine 97.6 0.0004 8.6E-09 70.4 10.0 94 108-219 548-642 (719)
46 PLN00207 polyribonucleotide nu 97.5 0.00021 4.6E-09 74.0 7.4 63 252-320 685-749 (891)
47 TIGR01952 nusA_arch NusA famil 97.5 0.0005 1.1E-08 56.0 7.5 103 144-288 34-136 (141)
48 KOG0336 ATP-dependent RNA heli 97.4 0.00031 6.7E-09 65.9 6.4 72 251-325 46-117 (629)
49 KOG1588 RNA-binding protein Sa 97.4 0.00015 3.2E-09 64.1 3.6 41 47-87 89-135 (259)
50 KOG0119 Splicing factor 1/bran 97.3 0.0017 3.8E-08 61.9 10.0 78 142-219 137-230 (554)
51 KOG0336 ATP-dependent RNA heli 97.2 0.00047 1E-08 64.7 5.4 56 45-103 42-97 (629)
52 PF14611 SLS: Mitochondrial in 97.2 0.023 5E-07 49.6 16.0 129 144-320 27-164 (210)
53 COG1185 Pnp Polyribonucleotide 97.2 0.00092 2E-08 66.6 7.5 65 252-322 552-617 (692)
54 TIGR03591 polynuc_phos polyrib 97.1 0.0023 5E-08 65.7 8.8 94 109-219 521-615 (684)
55 KOG2814 Transcription coactiva 97.0 0.00061 1.3E-08 62.0 3.8 71 49-125 56-126 (345)
56 KOG1588 RNA-binding protein Sa 97.0 0.0053 1.1E-07 54.5 9.0 42 249-290 89-136 (259)
57 KOG2814 Transcription coactiva 96.9 0.0013 2.8E-08 59.9 5.0 72 251-323 56-127 (345)
58 cd02134 NusA_KH NusA_K homolog 96.9 0.00093 2E-08 46.4 3.2 37 49-85 24-60 (61)
59 PRK04163 exosome complex RNA-b 96.8 0.0029 6.2E-08 56.4 6.5 66 253-324 146-212 (235)
60 PRK00106 hypothetical protein; 96.8 0.0067 1.5E-07 60.0 9.4 67 250-321 223-291 (535)
61 TIGR03319 YmdA_YtgF conserved 96.8 0.0067 1.4E-07 60.2 9.3 67 250-321 202-270 (514)
62 COG0195 NusA Transcription elo 96.8 0.0051 1.1E-07 52.7 7.2 101 146-289 79-179 (190)
63 PRK11824 polynucleotide phosph 96.8 0.0025 5.4E-08 65.5 6.3 63 252-320 554-617 (693)
64 COG0195 NusA Transcription elo 96.7 0.0065 1.4E-07 52.0 7.4 102 52-180 78-179 (190)
65 PRK12704 phosphodiesterase; Pr 96.7 0.0093 2E-07 59.3 9.4 67 250-321 208-276 (520)
66 cd02134 NusA_KH NusA_K homolog 96.7 0.0032 7E-08 43.7 4.3 36 252-287 25-60 (61)
67 PLN00207 polyribonucleotide nu 96.5 0.0073 1.6E-07 62.9 7.5 95 108-219 654-750 (891)
68 COG5176 MSL5 Splicing factor ( 96.5 0.0046 9.9E-08 52.7 4.7 43 46-88 144-192 (269)
69 COG1185 Pnp Polyribonucleotide 96.3 0.012 2.6E-07 58.9 7.7 96 108-220 521-617 (692)
70 PRK00468 hypothetical protein; 96.1 0.0051 1.1E-07 44.5 3.0 34 46-79 26-59 (75)
71 TIGR01953 NusA transcription t 96.1 0.02 4.3E-07 53.8 7.6 95 59-180 243-338 (341)
72 PRK12328 nusA transcription el 96.0 0.017 3.6E-07 54.5 6.6 96 59-182 251-347 (374)
73 PRK02821 hypothetical protein; 96.0 0.0064 1.4E-07 44.1 2.8 35 47-81 28-62 (77)
74 PRK12327 nusA transcription el 95.8 0.028 6.2E-07 53.1 7.1 96 59-181 245-341 (362)
75 PRK12328 nusA transcription el 95.7 0.024 5.2E-07 53.4 6.3 95 153-291 252-347 (374)
76 PRK11824 polynucleotide phosph 95.6 0.025 5.4E-07 58.3 6.6 95 108-219 523-618 (693)
77 COG5176 MSL5 Splicing factor ( 95.6 0.026 5.6E-07 48.2 5.4 40 143-182 148-193 (269)
78 PRK09202 nusA transcription el 95.6 0.031 6.7E-07 54.7 6.6 92 60-181 246-340 (470)
79 PRK01064 hypothetical protein; 95.5 0.015 3.3E-07 42.3 3.2 33 47-79 27-59 (78)
80 KOG1067 Predicted RNA-binding 95.4 0.032 6.9E-07 54.5 6.1 69 250-325 595-664 (760)
81 PRK12329 nusA transcription el 95.4 0.031 6.7E-07 53.6 6.0 95 59-180 277-372 (449)
82 COG1837 Predicted RNA-binding 95.4 0.016 3.4E-07 41.9 3.0 32 47-78 27-58 (76)
83 PRK12705 hypothetical protein; 95.4 0.045 9.7E-07 54.0 7.0 66 250-320 196-263 (508)
84 TIGR01953 NusA transcription t 95.3 0.05 1.1E-06 51.1 6.9 94 153-289 244-338 (341)
85 PRK09202 nusA transcription el 95.2 0.043 9.3E-07 53.7 6.2 103 144-290 232-340 (470)
86 PRK00468 hypothetical protein; 95.2 0.027 5.9E-07 40.7 3.6 32 250-281 28-59 (75)
87 PRK12327 nusA transcription el 95.1 0.06 1.3E-06 51.0 6.7 95 153-290 246-341 (362)
88 PRK04163 exosome complex RNA-b 95.0 0.061 1.3E-06 47.9 6.3 65 144-221 146-211 (235)
89 PRK02821 hypothetical protein; 95.0 0.031 6.6E-07 40.6 3.5 33 251-283 30-62 (77)
90 PRK12704 phosphodiesterase; Pr 94.9 0.048 1E-06 54.2 5.9 51 48-103 208-259 (520)
91 PRK12329 nusA transcription el 94.8 0.065 1.4E-06 51.5 6.2 103 144-289 264-372 (449)
92 PRK00106 hypothetical protein; 94.7 0.11 2.5E-06 51.5 7.7 64 144-219 226-291 (535)
93 TIGR03319 YmdA_YtgF conserved 94.6 0.11 2.4E-06 51.7 7.5 64 144-219 205-270 (514)
94 PF14611 SLS: Mitochondrial in 94.5 1.9 4.2E-05 37.5 14.5 130 53-221 29-167 (210)
95 KOG4369 RTK signaling protein 94.1 0.0093 2E-07 62.4 -1.3 72 253-324 1341-1413(2131)
96 COG1837 Predicted RNA-binding 94.0 0.069 1.5E-06 38.5 3.4 32 141-172 28-59 (76)
97 PRK01064 hypothetical protein; 93.7 0.088 1.9E-06 38.3 3.5 32 250-281 28-59 (78)
98 KOG3273 Predicted RNA-binding 93.4 0.23 4.9E-06 42.3 5.9 155 50-223 74-235 (252)
99 PF13083 KH_4: KH domain; PDB: 93.3 0.036 7.8E-07 39.8 1.0 35 47-81 26-60 (73)
100 cd02409 KH-II KH-II (K homolo 92.7 0.15 3.3E-06 35.3 3.5 35 49-83 24-58 (68)
101 PF13083 KH_4: KH domain; PDB: 91.9 0.09 2E-06 37.7 1.5 33 251-283 28-60 (73)
102 PF13184 KH_5: NusA-like KH do 91.4 0.22 4.7E-06 35.4 3.0 38 253-290 4-47 (69)
103 KOG3273 Predicted RNA-binding 91.2 0.14 3.1E-06 43.5 2.2 122 168-320 99-230 (252)
104 KOG1067 Predicted RNA-binding 91.1 0.69 1.5E-05 45.6 6.9 95 108-220 566-661 (760)
105 COG5166 Uncharacterized conser 90.9 0.49 1.1E-05 46.0 5.7 154 50-290 449-609 (657)
106 cd02410 archeal_CPSF_KH The ar 90.5 1.3 2.8E-05 36.1 7.1 90 159-290 22-114 (145)
107 PF13184 KH_5: NusA-like KH do 90.5 0.17 3.7E-06 35.9 1.8 36 52-87 5-46 (69)
108 KOG4369 RTK signaling protein 90.0 0.1 2.3E-06 55.0 0.4 71 49-124 1339-1410(2131)
109 PRK12705 hypothetical protein; 90.0 0.38 8.3E-06 47.6 4.3 41 48-88 196-237 (508)
110 cd02409 KH-II KH-II (K homolo 89.9 0.58 1.2E-05 32.3 4.1 34 252-285 25-58 (68)
111 KOG2874 rRNA processing protei 89.6 0.74 1.6E-05 41.3 5.3 51 155-219 161-211 (356)
112 KOG2874 rRNA processing protei 89.6 0.71 1.5E-05 41.4 5.2 51 264-321 161-211 (356)
113 cd02414 jag_KH jag_K homology 88.7 0.43 9.3E-06 34.6 2.8 34 51-84 25-58 (77)
114 cd02414 jag_KH jag_K homology 88.0 0.58 1.3E-05 33.9 3.1 36 252-287 24-59 (77)
115 COG5166 Uncharacterized conser 87.4 1.7 3.7E-05 42.4 6.6 127 156-325 393-528 (657)
116 PF07650 KH_2: KH domain syndr 87.2 0.39 8.5E-06 34.7 1.8 34 252-285 25-58 (78)
117 COG1097 RRP4 RNA-binding prote 87.0 1.9 4.2E-05 38.1 6.2 46 53-104 149-194 (239)
118 COG1097 RRP4 RNA-binding prote 86.9 1.8 4E-05 38.2 6.1 38 253-290 147-184 (239)
119 cd02413 40S_S3_KH K homology R 86.2 0.64 1.4E-05 34.1 2.4 36 51-86 31-66 (81)
120 PF07650 KH_2: KH domain syndr 85.7 0.61 1.3E-05 33.7 2.2 33 144-176 26-58 (78)
121 COG1855 ATPase (PilT family) [ 85.7 0.4 8.7E-06 46.3 1.4 39 50-88 486-524 (604)
122 PRK13764 ATPase; Provisional 85.2 0.48 1E-05 48.0 1.8 41 48-88 479-519 (602)
123 PRK13764 ATPase; Provisional 84.9 6.8 0.00015 39.8 9.8 43 143-185 481-523 (602)
124 COG1855 ATPase (PilT family) [ 84.6 2.5 5.3E-05 41.1 6.1 39 144-182 487-525 (604)
125 cd02410 archeal_CPSF_KH The ar 83.1 5.7 0.00012 32.4 6.8 92 67-181 23-114 (145)
126 PRK06418 transcription elongat 82.8 1.2 2.6E-05 37.4 2.9 38 49-87 60-97 (166)
127 PRK06418 transcription elongat 80.6 2.6 5.5E-05 35.4 4.1 39 252-291 61-99 (166)
128 cd02411 archeal_30S_S3_KH K ho 80.4 1.4 3E-05 32.6 2.2 28 52-79 40-67 (85)
129 cd02412 30S_S3_KH K homology R 80.0 1.2 2.6E-05 34.6 1.9 31 51-81 62-92 (109)
130 cd02413 40S_S3_KH K homology R 78.1 2.7 5.8E-05 30.8 3.1 37 252-288 30-66 (81)
131 COG1782 Predicted metal-depend 74.9 8.7 0.00019 37.8 6.4 96 63-181 42-137 (637)
132 COG0092 RpsC Ribosomal protein 74.3 2.2 4.9E-05 37.5 2.1 32 49-80 50-81 (233)
133 TIGR03675 arCOG00543 arCOG0054 72.4 7.6 0.00017 39.8 5.8 97 156-291 36-132 (630)
134 cd02412 30S_S3_KH K homology R 70.4 4.3 9.3E-05 31.5 2.7 30 254-283 63-92 (109)
135 cd02411 archeal_30S_S3_KH K ho 66.4 6.9 0.00015 28.8 3.0 28 254-281 40-67 (85)
136 TIGR03675 arCOG00543 arCOG0054 61.2 25 0.00055 36.1 6.9 95 64-181 37-131 (630)
137 COG1702 PhoH Phosphate starvat 59.1 26 0.00056 32.9 6.0 50 260-316 23-72 (348)
138 TIGR00436 era GTP-binding prot 56.4 13 0.00028 33.5 3.6 28 252-279 221-249 (270)
139 COG0092 RpsC Ribosomal protein 54.9 13 0.00027 32.9 3.0 28 144-171 52-79 (233)
140 PRK04191 rps3p 30S ribosomal p 52.4 11 0.00024 32.8 2.3 31 52-82 42-72 (207)
141 TIGR01008 rpsC_E_A ribosomal p 51.4 12 0.00026 32.3 2.4 31 51-81 39-69 (195)
142 COG1782 Predicted metal-depend 51.4 19 0.00041 35.6 3.9 97 155-290 41-137 (637)
143 COG1847 Jag Predicted RNA-bind 51.3 40 0.00087 29.3 5.5 36 252-287 91-126 (208)
144 CHL00048 rps3 ribosomal protei 51.3 12 0.00026 32.9 2.3 30 51-80 67-96 (214)
145 TIGR00436 era GTP-binding prot 50.7 14 0.0003 33.4 2.8 29 50-78 221-250 (270)
146 COG1159 Era GTPase [General fu 49.4 20 0.00044 32.9 3.6 37 252-288 229-274 (298)
147 COG1159 Era GTPase [General fu 49.2 16 0.00034 33.6 2.9 30 49-78 228-258 (298)
148 PRK15494 era GTPase Era; Provi 48.9 20 0.00043 33.7 3.6 37 252-288 273-318 (339)
149 PTZ00084 40S ribosomal protein 48.2 14 0.00029 32.6 2.2 33 51-83 45-77 (220)
150 COG1847 Jag Predicted RNA-bind 47.2 13 0.00028 32.2 1.9 38 48-85 89-126 (208)
151 PRK00089 era GTPase Era; Revie 46.7 23 0.00049 32.3 3.6 37 252-288 226-271 (292)
152 PF02749 QRPTase_N: Quinolinat 46.6 73 0.0016 23.4 5.7 52 270-321 32-86 (88)
153 PRK15494 era GTPase Era; Provi 45.8 18 0.00039 34.0 2.8 29 50-78 273-302 (339)
154 PF09869 DUF2096: Uncharacteri 44.2 78 0.0017 26.5 5.9 57 142-218 112-168 (169)
155 COG1702 PhoH Phosphate starvat 44.0 62 0.0013 30.4 5.9 51 150-214 22-72 (348)
156 PRK00089 era GTPase Era; Revie 40.4 33 0.00071 31.2 3.6 37 143-179 226-271 (292)
157 KOG1423 Ras-like GTPase ERA [C 39.7 22 0.00048 33.0 2.3 32 49-80 327-359 (379)
158 KOG1423 Ras-like GTPase ERA [C 39.0 61 0.0013 30.2 5.0 34 140-173 325-359 (379)
159 PTZ00084 40S ribosomal protein 36.8 54 0.0012 28.9 4.2 31 253-283 45-75 (220)
160 TIGR01008 rpsC_E_A ribosomal p 36.1 38 0.00082 29.2 3.1 29 253-281 39-67 (195)
161 PF00472 RF-1: RF-1 domain; I 35.6 92 0.002 24.2 5.0 52 65-125 22-73 (113)
162 TIGR01009 rpsC_bact ribosomal 34.1 30 0.00064 30.3 2.1 29 52-80 64-92 (211)
163 PF02749 QRPTase_N: Quinolinat 33.7 1.3E+02 0.0028 22.1 5.3 67 147-219 20-86 (88)
164 PRK04191 rps3p 30S ribosomal p 33.6 43 0.00093 29.2 3.1 30 254-283 42-71 (207)
165 CHL00048 rps3 ribosomal protei 33.2 43 0.00094 29.3 3.0 29 253-281 67-95 (214)
166 PRK15405 ethanolamine utilizat 32.3 2.6E+02 0.0056 24.5 7.5 121 194-323 82-211 (217)
167 PRK09256 hypothetical protein; 31.4 76 0.0017 25.7 4.0 60 65-126 23-99 (138)
168 COG4010 Uncharacterized protei 30.6 1.9E+02 0.0041 23.7 5.9 44 163-219 126-169 (170)
169 PRK03818 putative transporter; 27.8 6.5E+02 0.014 25.5 11.1 138 144-316 206-360 (552)
170 PF10369 ALS_ss_C: Small subun 27.2 1.7E+02 0.0037 20.8 4.8 43 271-317 16-58 (75)
171 PRK00310 rpsC 30S ribosomal pr 24.4 51 0.0011 29.3 2.0 30 51-80 63-92 (232)
172 TIGR01009 rpsC_bact ribosomal 22.7 85 0.0018 27.4 3.0 28 254-281 64-91 (211)
173 KOG3429 Predicted peptidyl-tRN 21.1 92 0.002 26.0 2.6 63 64-126 49-127 (172)
174 TIGR03802 Asp_Ala_antiprt aspa 20.7 8.9E+02 0.019 24.5 14.9 125 162-316 232-377 (562)
No 1
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=1e-38 Score=274.27 Aligned_cols=276 Identities=29% Similarity=0.455 Sum_probs=219.4
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCCCccccCCCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcce
Q 020173 16 VTEPEPRHDVSGKRRREDGEIEGSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEER 95 (330)
Q Consensus 16 ~~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~er 95 (330)
+.++.++.+..+||+.+|+. ..+. +...+.++||+.++.+|+||||+|+|||.|+.++++.|+|+++ ++++|
T Consensus 20 ~~~~~e~g~~~gkrp~~d~~---~qa~---k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~per 91 (390)
T KOG2192|consen 20 TFPNTETGGEFGKRPAEDME---EQAF---KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPER 91 (390)
T ss_pred cCCCCcccccccCCcchhhH---HHHh---hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCce
Confidence 45667777778999999986 2222 3356999999999999999999999999999999999999998 68999
Q ss_pred EEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCe
Q 020173 96 VIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT 175 (330)
Q Consensus 96 vi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~ 175 (330)
+|+|+... +.+-+-++.|.-.+.+.. .....+++||||+.+++|.|||++|+.||+|++++.++
T Consensus 92 i~tisad~-----~ti~~ilk~iip~lee~f-----------~~~~pce~rllihqs~ag~iigrngskikelrekcsar 155 (390)
T KOG2192|consen 92 ILTISADI-----ETIGEILKKIIPTLEEGF-----------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSAR 155 (390)
T ss_pred eEEEeccH-----HHHHHHHHHHhhhhhhCC-----------CCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhh
Confidence 99999874 334444444444443332 12245789999999999999999999999999999999
Q ss_pred EEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCC-cccCCC-----CCCCCCC-----------
Q 020173 176 IVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV-ISISPA-----YNYSAIR----------- 238 (330)
Q Consensus 176 I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~-~~~~~~-----~~~~~~~----------- 238 (330)
++|... |+ +++++|+|.+.|.+.+|..+++.|++.|.+.|.++. .+|.|+ |.|..+.
T Consensus 156 lkift~-----c~-p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pg 229 (390)
T KOG2192|consen 156 LKIFTE-----CC-PHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPG 229 (390)
T ss_pred hhhhhc-----cC-CCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCC
Confidence 999752 43 479999999999999999999999999999987763 223222 2222210
Q ss_pred C---------CCC-----------------C---------------------------CC-------------------C
Q 020173 239 P---------AQP-----------------F---------------------------VE-------------------P 246 (330)
Q Consensus 239 ~---------~~~-----------------~---------------------------~~-------------------~ 246 (330)
+ +.| | .+ +
T Consensus 230 papqrggqgpp~~~~sdlmay~r~GrpG~rydg~vdFs~detw~saidtw~~SewqmaYePQgGs~ydysyAG~~GsYGd 309 (390)
T KOG2192|consen 230 PAPQRGGQGPPPPRGSDLMAYDRRGRPGDRYDGMVDFSADETWPSAIDTWSPSEWQMAYEPQGGSGYDYSYAGGYGSYGD 309 (390)
T ss_pred CCCCCCCCCCCCCCccccceeccCCCCCccccccccccccccCCCcCCCcCccccccccCCCCCCCCCccccccccccCC
Confidence 0 000 0 00 0
Q ss_pred CCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 247 TSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 247 ~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
-.....+.++.||.++-|.|||++|+.|++|++++||.|++..+..++.+|+++|+||.+|++.|++|++.-+..
T Consensus 310 lGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~IkidepleGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 310 LGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred CCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcCCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 123457889999999999999999999999999999999999988889999999999999999999999877663
No 2
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.8e-36 Score=273.49 Aligned_cols=267 Identities=25% Similarity=0.441 Sum_probs=218.7
Q ss_pred CCCccccCCCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-CCCCcceEEEEecCCCCcchhHHHHHHH
Q 020173 38 GSDPKRRAKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQ 116 (330)
Q Consensus 38 ~~~~~~~~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervi~I~G~~~~~~~~~~~~A~~ 116 (330)
.+++..+....+..+|++||..++|.||||.|++||.|.+.|.|+|+|... ..+..|++++|-|++ +.+.+|+.
T Consensus 187 ~~G~~~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tp-----Eg~s~Ac~ 261 (584)
T KOG2193|consen 187 HSGPHHKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTP-----EGTSKACK 261 (584)
T ss_pred CCCCcccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCc-----cchHHHHH
Confidence 356666777889999999999999999999999999999999999999865 457889999999998 56789999
Q ss_pred HHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcE
Q 020173 117 QIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRV 196 (330)
Q Consensus 117 ~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~ 196 (330)
+|++++..+....... ....++++.++..+|++|||.|++||+|+.+||++|.|++-.++..+ +.+|.
T Consensus 262 ~ILeimqkEA~~~k~~--------~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y----npERT 329 (584)
T KOG2193|consen 262 MILEIMQKEAVDDKVA--------EEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY----NPERT 329 (584)
T ss_pred HHHHHHHHhhhccchh--------hhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc----Cccce
Confidence 9999998765433221 34578999999999999999999999999999999999986666553 68999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhhCCCCCCc------ccCCCCCCCCCCC-------CCCCCCC-------------CCCc
Q 020173 197 VQISGDVPAVLNALVEIGNQLRENPPRQVI------SISPAYNYSAIRP-------AQPFVEP-------------TSAD 250 (330)
Q Consensus 197 v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~------~~~~~~~~~~~~~-------~~~~~~~-------------~~~~ 250 (330)
|++.|+.++|.+|..+|+++|++....+.. ...|.+|.+..++ ..|+.+| ....
T Consensus 330 ItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe 409 (584)
T KOG2193|consen 330 ITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPE 409 (584)
T ss_pred EEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcc
Confidence 999999999999999999999987554421 1223333222211 1111111 1235
Q ss_pred ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-CCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-GEQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
....+|.||...+|+|||++|.+||.|.+.+||.|+|.++. ++..+|.|+|+|.+++.-+|+.+|...|.+
T Consensus 410 ~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGppeaqfKAQgrifgKikE 481 (584)
T KOG2193|consen 410 QEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPPEAQFKAQGRIFGKIKE 481 (584)
T ss_pred hhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCChHHHHhhhhhhhhhhhh
Confidence 57789999999999999999999999999999999999875 366799999999999999999999877765
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=1.5e-34 Score=273.88 Aligned_cols=254 Identities=24% Similarity=0.323 Sum_probs=206.0
Q ss_pred CCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (330)
Q Consensus 46 ~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~ 125 (330)
...-++.+..||...+|+||||+|+.|..|..++||+|++.....+..+|-|.+.|.+ +++..|..++.+++...
T Consensus 50 s~~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~p-----e~v~~aK~li~evv~r~ 124 (600)
T KOG1676|consen 50 SDTVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSP-----ENVEVAKQLIGEVVSRG 124 (600)
T ss_pred cccccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCc-----ccHHHHHHhhhhhhhcc
Confidence 3356788999999999999999999999999999999998776656789999999998 57788888888876554
Q ss_pred CCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH
Q 020173 126 DDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (330)
Q Consensus 126 ~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~ 205 (330)
...... ...-.....+.+++||...+|+||||+|++||.|++.+||++.+........ ..++.+.|+|+++.
T Consensus 125 ~~~~~~---~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~-----~~~KplritGdp~~ 196 (600)
T KOG1676|consen 125 RPPGGF---PDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT-----GADKPLRITGDPDK 196 (600)
T ss_pred CCCCCc---cccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC-----CCCCceeecCCHHH
Confidence 311110 0011134568999999999999999999999999999999999887654433 36788999999999
Q ss_pred HHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeE
Q 020173 206 VLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMI 285 (330)
Q Consensus 206 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I 285 (330)
|..|..+|.++|++......-+. ..++. ......+++|.||++.||.||||+|++||+|+.+||++|
T Consensus 197 ve~a~~lV~dil~e~~~~~~g~~-~~~g~------------~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KI 263 (600)
T KOG1676|consen 197 VEQAKQLVADILREEDDEVPGSG-GHAGV------------RGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKI 263 (600)
T ss_pred HHHHHHHHHHHHHhcccCCCccc-cccCc------------CccccceeEEeccccceeeEEecCchHHHHHhhccCcee
Confidence 99999999999997432211110 11111 112335899999999999999999999999999999999
Q ss_pred EEeCCCC-CCceeEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173 286 KVYGGKG-EQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQ 325 (330)
Q Consensus 286 ~i~~~~~-~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~ 325 (330)
+|.++.+ .+.+|.+.|.|+.++|+.|.+||.++|.+....
T Consensus 264 QfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 264 QFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred EeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 9998876 567999999999999999999999999887543
No 4
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=2.4e-34 Score=272.41 Aligned_cols=249 Identities=24% Similarity=0.371 Sum_probs=200.6
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-C-CCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-I-ARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~-~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~ 124 (330)
..+++..|+||++.+|+||||+|++||+|++.+||++.+-.. . ..+..+.+.|+|.+ ..++.|..+++++|.+
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp-----~~ve~a~~lV~dil~e 210 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP-----DKVEQAKQLVADILRE 210 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH-----HHHHHHHHHHHHHHHh
Confidence 456899999999999999999999999999999999987643 2 12267889999987 7889999999999987
Q ss_pred cCCCCcccc-ccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 020173 125 DDDSNSEAS-KVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (330)
Q Consensus 125 ~~~~~~~~~-~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~ 203 (330)
++....... ..........+.++-||+..||.||||+|++||+|+.+||++|+|.+ |..|. +.+|.+.|.|+.
T Consensus 211 ~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkp-Dd~p~-----speR~~~IiG~~ 284 (600)
T KOG1676|consen 211 EDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKP-DDDPS-----SPERPAQIIGTV 284 (600)
T ss_pred cccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeec-CCCCC-----CccceeeeecCH
Confidence 554432221 11111122348999999999999999999999999999999999975 44443 689999999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173 204 PAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGA 283 (330)
Q Consensus 204 ~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga 283 (330)
+.|..|.++|.++|.+..... ...++.+ .| .....+.|.||.+.+|.|||++|++||.|..+|||
T Consensus 285 d~ie~Aa~lI~eii~~~~~~~----~~~~~~G---------~P--~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA 349 (600)
T KOG1676|consen 285 DQIEHAAELINEIIAEAEAGA----GGGMGGG---------AP--GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGA 349 (600)
T ss_pred HHHHHHHHHHHHHHHHHhccC----CCCcCCC---------Cc--cceeeEEEeccccccccccCCCccchhhhcccCCc
Confidence 999999999999998762211 0001111 11 11138899999999999999999999999999999
Q ss_pred eEEEeCCC--CCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 284 MIKVYGGK--GEQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 284 ~I~i~~~~--~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
++.++++. .+..+++|+|+|++.+|+.|++||.+.+..
T Consensus 350 ~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~ 389 (600)
T KOG1676|consen 350 RCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGD 389 (600)
T ss_pred cccccCCCCCCCccceEEEEecCcccchHHHHHHHHHhcc
Confidence 99999872 245799999999999999999999988754
No 5
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=2.2e-31 Score=235.16 Aligned_cols=295 Identities=22% Similarity=0.304 Sum_probs=214.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCccccCCC-CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC---CCCC
Q 020173 17 TEPEPRHDVSGKRRREDGEIEGSDPKRRAKA-QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARH 92 (330)
Q Consensus 17 ~~~~~~~~~~~kr~~~~~~~~~~~~~~~~~~-~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~ 92 (330)
.+.+.+...+.||..+..+............ ..+.++||||+..+|.||||+|++|.+|+++|||+|++++. .|++
T Consensus 5 ~~~d~~~~~s~kr~~~a~pe~~~~k~~n~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGT 84 (402)
T KOG2191|consen 5 VPIDSDAPDSRKRPLEAPPEPGSTKRTNTGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGT 84 (402)
T ss_pred CcccCCCCCCccccccCCCCccccccccCCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCc
Confidence 3456666778888888766222222222222 34999999999999999999999999999999999999865 6899
Q ss_pred cceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccc--cccCCCcceEEEEEeeccccceecCCCChhHHHHHH
Q 020173 93 EERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASK--VAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRN 170 (330)
Q Consensus 93 ~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~--~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~ 170 (330)
.||||.|+|+- +.+...+.-|.++|.+.......... .+...++...+++++|+..+|.||||+|.+||.+++
T Consensus 85 TeRvcli~Gt~-----eai~av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~E 159 (402)
T KOG2191|consen 85 TERVCLIQGTV-----EALNAVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQE 159 (402)
T ss_pred cceEEEEeccH-----HHHHHHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHH
Confidence 99999999984 55666666667766654332111000 111233445799999999999999999999999999
Q ss_pred HhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCC---cccC----CCCCCCCCCCCCCC
Q 020173 171 SSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV---ISIS----PAYNYSAIRPAQPF 243 (330)
Q Consensus 171 ~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~---~~~~----~~~~~~~~~~~~~~ 243 (330)
++||+|+|++...... ...+|++++.|+++++.+|..+|+.+|.++|++.. .+|. +.-|+++. ..||
T Consensus 160 qsga~iqisPqkpt~~----sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya~vsGpvaNsnPt--Gspy 233 (402)
T KOG2191|consen 160 QSGAWIQISPQKPTGI----SLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYANVSGPVANSNPT--GSPY 233 (402)
T ss_pred hhCcceEecccCCCCc----cceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchhcccCcccccCCC--CCCC
Confidence 9999999995332111 14789999999999999999999999999998763 1111 11122211 1222
Q ss_pred CCC--CCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCceeEEEEEcCHHHHHHHHHHHHHH
Q 020173 244 VEP--TSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVALAKQRVDEY 318 (330)
Q Consensus 244 ~~~--~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v~I~Gt~~~v~~A~~~I~~~ 318 (330)
... ..........-++....|..-|.+|.++-.|...+|+.+.++...+ ....+ +.+.|.+-++..|-.+|...
T Consensus 234 a~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~g~gy~-~n~~g~~ls~~aa~g~L~~~ 312 (402)
T KOG2191|consen 234 AYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMAGYGYN-TNILGLGLSILAAEGVLAAK 312 (402)
T ss_pred CCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccccccccc-ccccchhhhhhhhhhHHHHh
Confidence 221 2233345567789999999999999999999999999999987533 33444 77888888888888877766
Q ss_pred HHHHH
Q 020173 319 IYSQL 323 (330)
Q Consensus 319 i~~~~ 323 (330)
...+.
T Consensus 313 ~~~a~ 317 (402)
T KOG2191|consen 313 VASAN 317 (402)
T ss_pred hcccC
Confidence 55443
No 6
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.98 E-value=2.1e-30 Score=248.96 Aligned_cols=265 Identities=30% Similarity=0.511 Sum_probs=202.1
Q ss_pred CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCC
Q 020173 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (330)
Q Consensus 48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~ 127 (330)
...++|||++.+.+|.||||+|..|++|+++|.++|+|.+..+++++|+++|+|...+....++.+|+.++.+.+.....
T Consensus 41 ~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 41 ETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred CcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhccc
Confidence 34559999999999999999999999999999999999999999999999999933322345566677666666554321
Q ss_pred ----CCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 020173 128 ----SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (330)
Q Consensus 128 ----~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~ 203 (330)
...+... ......+++||+||..++|.||||+|+.||+|+++|||+|.+... ++|.| ++|.|+|.|.+
T Consensus 121 ~d~~~~~d~~~--~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~s-----ter~V~IsG~~ 192 (485)
T KOG2190|consen 121 EDDEAAEDNGE--DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPNS-----TERAVTISGEP 192 (485)
T ss_pred ccccccccCCc--cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCcc-----cceeEEEcCch
Confidence 1111111 111124789999999999999999999999999999999999764 89985 78889999999
Q ss_pred HHHHHHHHHHHHHHhhCCCCC------CcccCC----------CCCCCC-----C--------------CCC--------
Q 020173 204 PAVLNALVEIGNQLRENPPRQ------VISISP----------AYNYSA-----I--------------RPA-------- 240 (330)
Q Consensus 204 ~~v~~A~~~I~~~i~~~~~~~------~~~~~~----------~~~~~~-----~--------------~~~-------- 240 (330)
++|.+|+..|...|.++++.. ...|.| ++.... . .+.
T Consensus 193 ~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~~~~~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g 272 (485)
T KOG2190|consen 193 DAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSASQGGPVLPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIG 272 (485)
T ss_pred HHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCcccccCccccccccCCcccccccccccchhhhhhhcCchhhceeeec
Confidence 999999999999999954221 122222 111000 0 000
Q ss_pred --------------------CCCCC----------C-----------------------CC-CcceEEEEEEccccccce
Q 020173 241 --------------------QPFVE----------P-----------------------TS-ADYVTFEMLISESLVGGL 266 (330)
Q Consensus 241 --------------------~~~~~----------~-----------------------~~-~~~~~~~v~IP~~~vg~I 266 (330)
.+... + .. ....+.++.||++++|+|
T Consensus 273 ~~~~~i~~l~~~~~~~i~v~~~~~~~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~~~~v~~~l~vps~~igci 352 (485)
T KOG2190|consen 273 KGGLVIRALRNETGASISVGDSRTDRIVTISARENPEDRYSMAQEALLLVQPRISENAGDDLTQTVTQRLLVPSDLIGCI 352 (485)
T ss_pred CCCccchhhhhhcCCceEeccccCcceeeeccccCcccccccchhhhhhccccccccccccccceeeeeeccCcccccee
Confidence 00000 0 00 233678999999999999
Q ss_pred ecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHH
Q 020173 267 IGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIY 320 (330)
Q Consensus 267 IGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~ 320 (330)
|||+|.+|.+|++.|||.|.|.+... ...++.++|+|+..+...|+.++...+.
T Consensus 353 iGk~G~~iseir~~tgA~I~I~~~~~~~~~~e~~~~I~~~~~~~~~~~~~~~~~~~ 408 (485)
T KOG2190|consen 353 IGKGGAKISEIRQRTGASISILNKEEVSGVREALVQITGMLREDLLAQYLIRARLS 408 (485)
T ss_pred ecccccchHHHHHhcCCceEEccccccCCcceeEEEecchhHHHHhhhhhcccccc
Confidence 99999999999999999999998766 6789999999999999999999865543
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.97 E-value=7.8e-31 Score=238.13 Aligned_cols=245 Identities=23% Similarity=0.358 Sum_probs=199.6
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC---CCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHh
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA---IARHEERVIIISSKDNDNVVSDAENALQQIAALIL 123 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~---~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~ 123 (330)
..+++++++..+.++|++|||.|.+||+|+++||++|.|++- .-.++||.|+|.|+- +.+..|-.+|...+.
T Consensus 277 ~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi-----Eac~~AE~eImkKlr 351 (584)
T KOG2193|consen 277 AEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI-----EACVQAEAEIMKKLR 351 (584)
T ss_pred hhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccH-----HHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999874 235689999999974 556666666666665
Q ss_pred hcCCCCc--------------------c------------ccccc--------cCCCcceEEEEEeeccccceecCCCCh
Q 020173 124 KDDDSNS--------------------E------------ASKVA--------AGHVAANTIRLLIAGSQAGCLIGMSGQ 163 (330)
Q Consensus 124 ~~~~~~~--------------------~------------~~~~~--------~~~~~~~~~~llip~~~~g~iIG~~G~ 163 (330)
+...... . +..+. ..+.....++++||...+|.|||++|.
T Consensus 352 e~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~ 431 (584)
T KOG2193|consen 352 ECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQ 431 (584)
T ss_pred HHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcch
Confidence 4322100 0 00000 112345678999999999999999999
Q ss_pred hHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCC
Q 020173 164 NIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPF 243 (330)
Q Consensus 164 ~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (330)
+||.|...+|+.|+|.+.+ .|. ..+|.|+|+|++++..+|..+|..+|.+...
T Consensus 432 hIKql~RfagASiKIappE-~pd-----vseRMViItGppeaqfKAQgrifgKikEenf--------------------- 484 (584)
T KOG2193|consen 432 HIKQLSRFAGASIKIAPPE-IPD-----VSERMVIITGPPEAQFKAQGRIFGKIKEENF--------------------- 484 (584)
T ss_pred hHHHHHHhccceeeecCCC-CCC-----cceeEEEecCChHHHHhhhhhhhhhhhhhcc---------------------
Confidence 9999999999999998654 444 5789999999999999999999999988721
Q ss_pred CCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 244 VEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 244 ~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
..|.........+.||...+|+||||||.++++|+..|+|.+.||++.. +.+.-+|.|.|.....+.|+..|.+++..
T Consensus 485 ~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdqtpdEnd~vivriiGhfyatq~aQrki~~iv~q 564 (584)
T KOG2193|consen 485 FLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQTPDENDQVIVRIIGHFYATQNAQRKIAHIVNQ 564 (584)
T ss_pred CCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccCCCCccceeeeeeechhhcchHHHHHHHHHHHH
Confidence 1123455678899999999999999999999999999999999998754 34567889999999999999999999876
Q ss_pred HH
Q 020173 322 QL 323 (330)
Q Consensus 322 ~~ 323 (330)
.-
T Consensus 565 vk 566 (584)
T KOG2193|consen 565 VK 566 (584)
T ss_pred HH
Confidence 54
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.92 E-value=3.8e-24 Score=189.47 Aligned_cols=168 Identities=26% Similarity=0.375 Sum_probs=139.6
Q ss_pred cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC-CCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP-NQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~-~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 219 (330)
..+.+++|||+..+|.||||+|++|.+|+.++||+|++++. |.+|. .+||+|.|+|+.+++....+.|+++|++
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG-----TTeRvcli~Gt~eai~av~efI~dKire 111 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG-----TTERVCLIQGTVEALNAVHEFIADKIRE 111 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC-----ccceEEEEeccHHHHHHHHHHHHHHHHH
Confidence 34789999999999999999999999999999999999874 44564 7999999999999999999999999999
Q ss_pred CCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC---CCce
Q 020173 220 NPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG---EQKH 296 (330)
Q Consensus 220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~---~~~~ 296 (330)
.+......+ -..+|.- .+....+++.+|+.-+|.||||+|.+||.+++++||+|+|.+.++ .-.+
T Consensus 112 ~p~~~~k~v---------~~~~pqt---~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqe 179 (402)
T KOG2191|consen 112 KPQAVAKPV---------DILQPQT---PDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQE 179 (402)
T ss_pred hHHhhcCCc---------cccCCCC---ccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCCCCcccee
Confidence 865431100 0011111 112245899999999999999999999999999999999996543 3369
Q ss_pred eEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173 297 RHIQFGGSAQQVALAKQRVDEYIYSQLIQ 325 (330)
Q Consensus 297 r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~ 325 (330)
|+|+++|.+++..+|..+|++.|.++...
T Consensus 180 rvvt~sge~e~~~~A~~~IL~Ki~eDpqs 208 (402)
T KOG2191|consen 180 RVVTVSGEPEQNMKAVSLILQKIQEDPQS 208 (402)
T ss_pred EEEEecCCHHHHHHHHHHHHHHhhcCCcc
Confidence 99999999999999999999999876544
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.81 E-value=8.5e-19 Score=168.98 Aligned_cols=157 Identities=29% Similarity=0.446 Sum_probs=132.2
Q ss_pred eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc---------CHHHHHHHHHHH
Q 020173 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG---------DVPAVLNALVEI 213 (330)
Q Consensus 143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G---------~~~~v~~A~~~I 213 (330)
.+.|+|++-..+|.|||++|..+++|+.++.++|.+... .+.| .+|+++|+| ..+++.+|..+|
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~--~~~c-----~eRIiti~g~~~~~~~~~~~~al~ka~~~i 115 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNES--LPGC-----PERIITITGNRVELNLSPATDALFKAFDMI 115 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecC--CCCC-----CcceEEEecccccccCCchHHHHHHHHHHH
Confidence 358999999999999999999999999999999998643 5665 689999999 999999999999
Q ss_pred HHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-C
Q 020173 214 GNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-G 292 (330)
Q Consensus 214 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~ 292 (330)
...++++.... .+.+. .......+++|+||..++|.||||+|+.||+|+++|||+|.+..+. +
T Consensus 116 v~~~~~d~~~~-----~d~~~-----------~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~~lP 179 (485)
T KOG2190|consen 116 VFKLEEDDEAA-----EDNGE-----------DASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSDMLP 179 (485)
T ss_pred hhccccccccc-----ccCCc-----------cccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCCCCC
Confidence 99877442110 01110 1112247899999999999999999999999999999999999873 4
Q ss_pred CCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173 293 EQKHRHIQFGGSAQQVALAKQRVDEYIYSQ 322 (330)
Q Consensus 293 ~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~ 322 (330)
.+++|.|+|+|.++.|..|...|...|.+-
T Consensus 180 ~ster~V~IsG~~~av~~al~~Is~~L~~~ 209 (485)
T KOG2190|consen 180 NSTERAVTISGEPDAVKKALVQISSRLLEN 209 (485)
T ss_pred cccceeEEEcCchHHHHHHHHHHHHHHHhc
Confidence 678999999999999999999999998873
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.72 E-value=3.4e-17 Score=141.63 Aligned_cols=150 Identities=27% Similarity=0.463 Sum_probs=133.1
Q ss_pred ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCC
Q 020173 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENP 221 (330)
Q Consensus 142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~ 221 (330)
.+++++|+.++.+|.||||+|++||.|+.++++.|++.... ..+|+++|+.+.+.|.+.++.|+..|++.+
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~---------~peri~tisad~~ti~~ilk~iip~lee~f 117 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS---------GPERILTISADIETIGEILKKIIPTLEEGF 117 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC---------CCceeEEEeccHHHHHHHHHHHhhhhhhCC
Confidence 35899999999999999999999999999999999996432 578999999999999999999999998874
Q ss_pred CCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC-CCCceeEEE
Q 020173 222 PRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK-GEQKHRHIQ 300 (330)
Q Consensus 222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~-~~~~~r~v~ 300 (330)
.. ......+++|..+++|.|||++|+.||+|++.-.|+++|--.. +++++|+|.
T Consensus 118 ~~-------------------------~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~c~p~stdrv~l 172 (390)
T KOG2192|consen 118 QL-------------------------PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVL 172 (390)
T ss_pred CC-------------------------CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhccCCCCcceEEE
Confidence 32 1347789999999999999999999999999999999998764 478899999
Q ss_pred EEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173 301 FGGSAQQVALAKQRVDEYIYSQLIQ 325 (330)
Q Consensus 301 I~Gt~~~v~~A~~~I~~~i~~~~~~ 325 (330)
|.|.+.+|-.+.+.|.++|.+..++
T Consensus 173 ~~g~~k~v~~~i~~il~~i~e~pik 197 (390)
T KOG2192|consen 173 IGGKPKRVVECIKIILDLISESPIK 197 (390)
T ss_pred ecCCcchHHHHHHHHHHHhhcCCcC
Confidence 9999999999999999988765443
No 11
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.72 E-value=8.7e-17 Score=136.07 Aligned_cols=138 Identities=25% Similarity=0.400 Sum_probs=108.4
Q ss_pred EEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEE---EcCHHHHHHHHHHHHHHHhhCCCC
Q 020173 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI---SGDVPAVLNALVEIGNQLRENPPR 223 (330)
Q Consensus 147 llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I---~G~~~~v~~A~~~I~~~i~~~~~~ 223 (330)
+.||...+|.|||++|++|+.|+++||++|.+.. ++..|.| +++++++.+|..+|..+.....+.
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~------------~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDS------------ETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEc------------CCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence 5689999999999999999999999999999974 2356777 889999999999999987753211
Q ss_pred CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEcc---------ccccceecCCCchHHHHHHHhCCeEEEeCCCCCC
Q 020173 224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE---------SLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQ 294 (330)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~---------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~ 294 (330)
..+.. + ...+...-+.|+. ...|+|||++|++++.|+..|||+|.|+.
T Consensus 70 ~A~~l---~---------------gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~----- 126 (172)
T TIGR03665 70 KALKL---L---------------DDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG----- 126 (172)
T ss_pred HHHHh---c---------------CCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC-----
Confidence 00000 0 0112222334444 36899999999999999999999999984
Q ss_pred ceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 295 KHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 295 ~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
..|.|.|++++++.|+.+|.++|..
T Consensus 127 --~~v~i~G~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 127 --KTVGIIGDPEQVQIAREAIEMLIEG 151 (172)
T ss_pred --CEEEEECCHHHHHHHHHHHHHHHcC
Confidence 5799999999999999999998843
No 12
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.67 E-value=1.3e-15 Score=129.86 Aligned_cols=141 Identities=26% Similarity=0.380 Sum_probs=108.6
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE----cCHHHHHHHHHHHHHHHhh
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS----GDVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~----G~~~~v~~A~~~I~~~i~~ 219 (330)
...+.||...++.|||++|++|+.|+++||++|.+.. ++..|.|. ++++++.+|..+|.++...
T Consensus 4 ~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~------------~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDS------------ETGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred eEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEEC------------CCCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 6788999999999999999999999999999999973 23567784 8999999999999998875
Q ss_pred CCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEcc---------ccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 220 NPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISE---------SLVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 220 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~---------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
..+...+.. ++ ..+...-+.|.. ..+|+|||++|++++.|++.|||+|.|..
T Consensus 72 f~~e~A~~l---~g---------------d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~- 132 (180)
T PRK13763 72 FSPEKALRL---LD---------------DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG- 132 (180)
T ss_pred CCHHHHHHH---hC---------------CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC-
Confidence 211100000 00 011111111211 36899999999999999999999999984
Q ss_pred CCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 291 KGEQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 291 ~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
..|.|.|++++++.|+..|..++..
T Consensus 133 ------~~v~i~G~~~~~~~A~~~I~~li~g 157 (180)
T PRK13763 133 ------KTVAIIGDPEQVEIAREAIEMLIEG 157 (180)
T ss_pred ------CEEEEEeCHHHHHHHHHHHHHHHcC
Confidence 2389999999999999999988743
No 13
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=99.64 E-value=1.3e-15 Score=128.87 Aligned_cols=140 Identities=21% Similarity=0.289 Sum_probs=104.1
Q ss_pred EEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEE---ecCCCCcchhHHHHHHHHHHHHHhhcCCCCc
Q 020173 54 IIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIII---SSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (330)
Q Consensus 54 i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I---~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~ 130 (330)
|.||.+.+|.|||++|++|+.|+++|||+|+|.+. +..|.| ++++ ..+.+|...|..+.......
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~-----~~i~kA~~~I~~i~~gf~~e-- 69 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDP-----LAVMKAREVVKAIGRGFSPE-- 69 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCH-----HHHHHHHHHHHHHHcCCCHH--
Confidence 57899999999999999999999999999999863 345777 3332 67888888888865532211
Q ss_pred cccccccCCCcceEEE-EEeec---------cccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE
Q 020173 131 EASKVAAGHVAANTIR-LLIAG---------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS 200 (330)
Q Consensus 131 ~~~~~~~~~~~~~~~~-llip~---------~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~ 200 (330)
++... .+ ..+... +-|+. ...|+|||++|++++.|++.|||+|.+. +..|.|.
T Consensus 70 ~A~~l-~g--d~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~--------------~~~v~i~ 132 (172)
T TIGR03665 70 KALKL-LD--DDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY--------------GKTVGII 132 (172)
T ss_pred HHHHh-cC--CcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc--------------CCEEEEE
Confidence 00000 00 011111 22222 3689999999999999999999999984 2579999
Q ss_pred cCHHHHHHHHHHHHHHHhhCCC
Q 020173 201 GDVPAVLNALVEIGNQLRENPP 222 (330)
Q Consensus 201 G~~~~v~~A~~~I~~~i~~~~~ 222 (330)
|+++++..|...|.+++.+.++
T Consensus 133 G~~~~~~~A~~~i~~li~~~~~ 154 (172)
T TIGR03665 133 GDPEQVQIAREAIEMLIEGAPH 154 (172)
T ss_pred CCHHHHHHHHHHHHHHHcCCCC
Confidence 9999999999999999976643
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.60 E-value=1.1e-14 Score=124.21 Aligned_cols=147 Identities=21% Similarity=0.270 Sum_probs=106.5
Q ss_pred eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (330)
Q Consensus 50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~ 129 (330)
+...+.||.+.+|.|||++|++|+.|+++|||+|++.+. +..|.|.... ......+.+|...|..+.......
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~-~~d~~~i~kA~~~I~ai~~gf~~e- 75 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTD-GEDPLAVLKARDIVKAIGRGFSPE- 75 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCC-CCCHHHHHHHHHHHHHHhcCCCHH-
Confidence 467899999999999999999999999999999999873 3556775111 001367888888888876532211
Q ss_pred ccccccccCCCcceEEEE-E----ee-----ccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEE
Q 020173 130 SEASKVAAGHVAANTIRL-L----IA-----GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQI 199 (330)
Q Consensus 130 ~~~~~~~~~~~~~~~~~l-l----ip-----~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I 199 (330)
++... .+ ..+...+ - .+ ...+|+|||++|++++.|++.|||+|.+.. +.|.|
T Consensus 76 -~A~~l-~g--d~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~--------------~~v~i 137 (180)
T PRK13763 76 -KALRL-LD--DDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG--------------KTVAI 137 (180)
T ss_pred -HHHHH-hC--CCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC--------------CEEEE
Confidence 00000 00 0011111 0 11 136899999999999999999999999852 34889
Q ss_pred EcCHHHHHHHHHHHHHHHhhCC
Q 020173 200 SGDVPAVLNALVEIGNQLRENP 221 (330)
Q Consensus 200 ~G~~~~v~~A~~~I~~~i~~~~ 221 (330)
.|+++++..|...|..+++...
T Consensus 138 ~G~~~~~~~A~~~I~~li~g~~ 159 (180)
T PRK13763 138 IGDPEQVEIAREAIEMLIEGAP 159 (180)
T ss_pred EeCHHHHHHHHHHHHHHHcCCC
Confidence 9999999999999999997653
No 15
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.51 E-value=4.6e-14 Score=100.11 Aligned_cols=63 Identities=32% Similarity=0.475 Sum_probs=58.8
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC-CCceeEEEEEcCHHHHHHHHHHH
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG-EQKHRHIQFGGSAQQVALAKQRV 315 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~-~~~~r~v~I~Gt~~~v~~A~~~I 315 (330)
+++|.||.+++|+|||++|++|++|+++|||+|.+.++.. .+.+|+|+|.|++++++.|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999998765 57799999999999999999987
No 16
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.42 E-value=1e-12 Score=124.36 Aligned_cols=243 Identities=23% Similarity=0.317 Sum_probs=173.3
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~ 126 (330)
..++.+++.||...+-.++|++|.+|+.|+..++++|.+.+.. -.++++..+.|-+ ..+..|...+..++...
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p-----~~v~~a~a~~~~~~~~~- 137 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFP-----VQVCKAKAAIHQILTEN- 137 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCC-----CCCChHHHHHHHHHhcC-
Confidence 3678999999999999999999999999999999999997652 2356666666543 23344444445544332
Q ss_pred CCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 020173 127 DSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (330)
Q Consensus 127 ~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v 206 (330)
..+...+-+|...++.|+|++|++++.++..++++|.+.... .| .-.+...|.|....+
T Consensus 138 --------------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~----g~~~~~~i~~qqk~~ 196 (608)
T KOG2279|consen 138 --------------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RL----GLSRLIKISGQQKEV 196 (608)
T ss_pred --------------Ccccccccchhhhcccccccchhhhcchhccccccccccccc---cc----ccccceecccccchH
Confidence 234567789999999999999999999999999999986432 22 346788899998888
Q ss_pred HHHHHHHHHHHhhCCC---------------CCCccc------------CC---CCCCCCCCCCCC--------------
Q 020173 207 LNALVEIGNQLRENPP---------------RQVISI------------SP---AYNYSAIRPAQP-------------- 242 (330)
Q Consensus 207 ~~A~~~I~~~i~~~~~---------------~~~~~~------------~~---~~~~~~~~~~~~-------------- 242 (330)
..|..++.+.+.++-. +...+. .+ .+...+..++.+
T Consensus 197 ~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vs 276 (608)
T KOG2279|consen 197 AAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVS 276 (608)
T ss_pred HHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEe
Confidence 8999999988866411 110000 00 000000011100
Q ss_pred ----------CCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCc---eeEEEEEcCHHHHH
Q 020173 243 ----------FVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQK---HRHIQFGGSAQQVA 309 (330)
Q Consensus 243 ----------~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~---~r~v~I~Gt~~~v~ 309 (330)
-..+.........|.||..++|.|||+.|+.++.+...|++.+.|.-..-... -.++.+.|+..-++
T Consensus 277 k~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh~~n 356 (608)
T KOG2279|consen 277 KEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQHYEN 356 (608)
T ss_pred cccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhHHHH
Confidence 00112334456799999999999999999999999999999999986432221 25678999999999
Q ss_pred HHHHHHHH
Q 020173 310 LAKQRVDE 317 (330)
Q Consensus 310 ~A~~~I~~ 317 (330)
.|..++..
T Consensus 357 ~vl~ml~~ 364 (608)
T KOG2279|consen 357 SVLEMLTV 364 (608)
T ss_pred HHHhhhhc
Confidence 99988863
No 17
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.41 E-value=4.9e-13 Score=93.30 Aligned_cols=60 Identities=35% Similarity=0.552 Sum_probs=55.6
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHH
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRV 315 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I 315 (330)
|.+|.||.+++|+|||++|++|++|++.|||+|.|+++ + .+..|+|+|++++|+.|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~--~-~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD--D-ERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST--T-EEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC--C-CcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999975 3 566999999999999999886
No 18
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=99.39 E-value=5.7e-13 Score=94.50 Aligned_cols=63 Identities=44% Similarity=0.685 Sum_probs=56.6
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCC-CCcceEEEEecCCCCcchhHHHHHHHHH
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIA-RHEERVIIISSKDNDNVVSDAENALQQI 118 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~-~~~ervi~I~G~~~~~~~~~~~~A~~~i 118 (330)
+++|+||.+.+|+|||++|.+|++|+++|||+|++++... +..+|+|+|.|+. +++.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~~~~~~r~v~I~G~~-----~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKP-----SAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCCCCCCceEEEEEeCH-----HHHHHHHHhh
Confidence 3799999999999999999999999999999999998754 6789999999985 7788888776
No 19
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.38 E-value=7.6e-13 Score=92.96 Aligned_cols=61 Identities=31% Similarity=0.388 Sum_probs=56.1
Q ss_pred EEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHH
Q 020173 254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVD 316 (330)
Q Consensus 254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~ 316 (330)
.+|.||..++|+|||++|++|++|+++|||+|.+++.. +.++.|+|+|++++|..|+.+|+
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--~~~~~v~I~G~~~~v~~A~~~i~ 62 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--SKSDTITITGPKENVEKAKEEIL 62 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--CCCCEEEEEcCHHHHHHHHHHhC
Confidence 57899999999999999999999999999999999754 56789999999999999998873
No 20
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=99.33 E-value=4.1e-12 Score=89.61 Aligned_cols=62 Identities=35% Similarity=0.560 Sum_probs=57.8
Q ss_pred EEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHH
Q 020173 254 FEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRV 315 (330)
Q Consensus 254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I 315 (330)
.+|.||..++++|||++|++|++|++.|||+|.|++...+..++.|+|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCHHHHHHHHHHh
Confidence 57999999999999999999999999999999999866566789999999999999999887
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.31 E-value=5.8e-12 Score=87.96 Aligned_cols=59 Identities=22% Similarity=0.321 Sum_probs=53.9
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVD 316 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~ 316 (330)
.+..|.||.+++|+|||++|++|++|++.|||+|.+++ ++.|.|+|+ +++++.|+.+|+
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 45689999999999999999999999999999999996 357999999 999999999873
No 22
>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=99.14 E-value=1e-10 Score=82.05 Aligned_cols=60 Identities=27% Similarity=0.362 Sum_probs=54.1
Q ss_pred EEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 020173 145 IRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (330)
Q Consensus 145 ~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I 213 (330)
..+.||..++++|||++|++|++|+++|||+|.++..+ ..++.|+|+|+.++|..|..+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~---------~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPG---------SKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCCC---------CCCCEEEEEcCHHHHHHHHHHh
Confidence 57889999999999999999999999999999997542 3578899999999999999887
No 23
>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=99.12 E-value=1.4e-10 Score=81.79 Aligned_cols=62 Identities=44% Similarity=0.665 Sum_probs=53.5
Q ss_pred EEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHH
Q 020173 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQI 118 (330)
Q Consensus 52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i 118 (330)
.+|.||.+++++|||++|++|++|+++|||+|.|++......++.|.|.|+. +++..|..++
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~~~~~~~v~i~G~~-----~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTP-----EAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCCCCCceEEEEEcCH-----HHHHHHHHHh
Confidence 6899999999999999999999999999999999986545678999999984 5666666554
No 24
>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=99.12 E-value=1.4e-10 Score=80.81 Aligned_cols=60 Identities=32% Similarity=0.445 Sum_probs=53.5
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHH
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEI 213 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I 213 (330)
|.+|.||..++++|||++|++|++|+++|||+|.++.. .....|+|.|+.++|.+|+++|
T Consensus 1 T~~i~vp~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~----------~~~~~v~I~G~~~~v~~A~~~I 60 (60)
T PF00013_consen 1 TERIEVPSSLVGRIIGKKGSNIKEIEEETGVKIQIPDD----------DERDIVTISGSPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEEHHHHHHHHTGGGHHHHHHHHHHTSEEEEEST----------TEEEEEEEEESHHHHHHHHHHH
T ss_pred CEEEEECHHHcCEEECCCCCcHHHhhhhcCeEEEEcCC----------CCcEEEEEEeCHHHHHHHHhhC
Confidence 57899999999999999999999999999999999743 1234899999999999999876
No 25
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.10 E-value=8.7e-10 Score=112.59 Aligned_cols=229 Identities=21% Similarity=0.240 Sum_probs=158.9
Q ss_pred eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCC--cchhHHHHHHHHHHHHHhh---
Q 020173 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDND--NVVSDAENALQQIAALILK--- 124 (330)
Q Consensus 50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~--~~~~~~~~A~~~i~~~i~~--- 124 (330)
+..++.+-...+.++||++|.++..++.++.+.++|++... ......+.|.... ........++.++..-...
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~--~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~ 278 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNK--SSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEI 278 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEcccccc--cchhhhhccccccceehhhhhHHHHHHhcChhhhhhh
Confidence 78899999999999999999999999999999999997632 2222233331110 0012233443332221100
Q ss_pred ---cCC---C--------------------Ccc------c-----cccc-------------cCCCcceEEEEEeecccc
Q 020173 125 ---DDD---S--------------------NSE------A-----SKVA-------------AGHVAANTIRLLIAGSQA 154 (330)
Q Consensus 125 ---~~~---~--------------------~~~------~-----~~~~-------------~~~~~~~~~~llip~~~~ 154 (330)
... . ... . .... ..........+.+....+
T Consensus 279 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~ 358 (753)
T KOG2208|consen 279 IYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEEL 358 (753)
T ss_pred hhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhh
Confidence 000 0 000 0 0000 011233567777888889
Q ss_pred ceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCC
Q 020173 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY 234 (330)
Q Consensus 155 g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 234 (330)
..++|++|.+|.+|++++.+.+.+.... +++..+.++|...++.+|...+...+.+-+.
T Consensus 359 ~~v~GK~~~ni~ki~e~~~~~i~~~~~~---------~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------------ 417 (753)
T KOG2208|consen 359 KFVIGKKGANIEKIREESQVKIDLPKQG---------SNNKKVVITGVSANDEKAVEDVEKIIAEILN------------ 417 (753)
T ss_pred hhhcCCCCccHHHHHHhhhhceeccccc---------CCCCCeEEeccccchhHHHHHHHHHHHhhhc------------
Confidence 9999999999999999999999986532 4677899999999999999999999987621
Q ss_pred CCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhC-CeEEEeCCCCCCceeEEEEEcCHHHHHHHHH
Q 020173 235 SAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESG-AMIKVYGGKGEQKHRHIQFGGSAQQVALAKQ 313 (330)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tg-a~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~ 313 (330)
......+.||...+..|||.+|..|++|...++ .+|+.+.+ ......+++.|....+..+..
T Consensus 418 ---------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~--~~~~~~~~~~~~~~dv~~~~~ 480 (753)
T KOG2208|consen 418 ---------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNN--NNSSDMVTIRGISKDVEKSVS 480 (753)
T ss_pred ---------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCC--CcccccceEeccccccchhHH
Confidence 124567999999999999999999999999999 56666654 444456777787777776555
Q ss_pred HHHHH
Q 020173 314 RVDEY 318 (330)
Q Consensus 314 ~I~~~ 318 (330)
+...+
T Consensus 481 ~~~~~ 485 (753)
T KOG2208|consen 481 LLKAL 485 (753)
T ss_pred HHHhh
Confidence 55443
No 26
>PF13014 KH_3: KH domain
Probab=99.06 E-value=2.7e-10 Score=73.73 Aligned_cols=42 Identities=36% Similarity=0.619 Sum_probs=38.0
Q ss_pred cccceecCCCchHHHHHHHhCCeEEEeC-CCCCCceeEEEEEc
Q 020173 262 LVGGLIGRCGSNISRIRNESGAMIKVYG-GKGEQKHRHIQFGG 303 (330)
Q Consensus 262 ~vg~IIGk~G~~Ik~i~~~tga~I~i~~-~~~~~~~r~v~I~G 303 (330)
+||+|||++|++|++|+++|||+|+|++ ...++.++.|+|+|
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 33467899999998
No 27
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=99.03 E-value=3.3e-09 Score=89.33 Aligned_cols=151 Identities=17% Similarity=0.204 Sum_probs=108.9
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCC
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDS 128 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~ 128 (330)
.....+.||....+.+||+.|+..+.|++.++++|.++. .+..+.|..+.........++|...+..+-...+..
T Consensus 7 ~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrGF~pe 81 (194)
T COG1094 7 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 455679999999999999999999999999999999986 356677776632112355677777666654433221
Q ss_pred CccccccccCCCcceEEEE-----Eee------ccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEE
Q 020173 129 NSEASKVAAGHVAANTIRL-----LIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVV 197 (330)
Q Consensus 129 ~~~~~~~~~~~~~~~~~~l-----lip------~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v 197 (330)
....... ....+.+ ++. ....|+|||++|.+.+.|++.|+|.|.+. +..|
T Consensus 82 ~A~~LL~-----d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~--------------g~tV 142 (194)
T COG1094 82 KALKLLE-----DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY--------------GKTV 142 (194)
T ss_pred HHHHHhc-----CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe--------------CcEE
Confidence 1100000 0001111 111 12459999999999999999999999996 3479
Q ss_pred EEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173 198 QISGDVPAVLNALVEIGNQLRENPPR 223 (330)
Q Consensus 198 ~I~G~~~~v~~A~~~I~~~i~~~~~~ 223 (330)
.|-|..++|..|.+.|..++...++.
T Consensus 143 aiiG~~~~v~iAr~AVemli~G~~h~ 168 (194)
T COG1094 143 AIIGGFEQVEIAREAVEMLINGAPHG 168 (194)
T ss_pred EEecChhhhHHHHHHHHHHHcCCCch
Confidence 99999999999999999999887654
No 28
>smart00322 KH K homology RNA-binding domain.
Probab=99.03 E-value=1.9e-09 Score=76.36 Aligned_cols=66 Identities=32% Similarity=0.505 Sum_probs=59.7
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYI 319 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i 319 (330)
.+.+|.||..++|.+||++|++|++|++.||++|.++.... ....++|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--EERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCC--CccEEEEEcCHHHHHHHHHHHHHHh
Confidence 57789999999999999999999999999999999986432 5688999999999999999998765
No 29
>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=99.03 E-value=1.3e-09 Score=76.03 Aligned_cols=57 Identities=26% Similarity=0.274 Sum_probs=51.7
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHH
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEI 213 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I 213 (330)
...+.||...++.|||++|++|+.|+++|||+|.+.. ++.|.|.|+ .+++..|..+|
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-------------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-------------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-------------CCEEEEEeCCHHHHHHHHHHh
Confidence 5678899999999999999999999999999999852 457999998 99999999886
No 30
>PF13014 KH_3: KH domain
Probab=99.03 E-value=3.3e-10 Score=73.28 Aligned_cols=42 Identities=43% Similarity=0.673 Sum_probs=38.2
Q ss_pred ccceeecccChhhhhhhhccCcEEEEec-CCCCCcceEEEEec
Q 020173 60 QIGKVIGKEGHRIQKIREETKATIKIAD-AIARHEERVIIISS 101 (330)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~tg~~I~i~~-~~~~~~ervi~I~G 101 (330)
++|+|||++|.+|++|+++|||+|+|++ ..++..+++|+|+|
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 45577899999987
No 31
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.86 E-value=4.9e-08 Score=82.37 Aligned_cols=141 Identities=26% Similarity=0.377 Sum_probs=106.5
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-----CHHHHHHHHHHHHHHHh
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-----DVPAVLNALVEIGNQLR 218 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G-----~~~~v~~A~~~I~~~i~ 218 (330)
...+.||....+.++|+.|+..+.|.+.+++++.+.. .+..|.|.. ++..+++|...|.++-+
T Consensus 9 ~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~------------~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgr 76 (194)
T COG1094 9 SEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS------------KTGSVTIRTTRKTEDPLALLKARDVVKAIGR 76 (194)
T ss_pred eeeeecCchhheeeecccccchHHHHhhcCeEEEEEC------------CCCeEEEEecCCCCChHHHHHHHHHHHHHhc
Confidence 5678999999999999999999999999999999974 345566643 68999999999988877
Q ss_pred hCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEE------cc----ccccceecCCCchHHHHHHHhCCeEEEe
Q 020173 219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLI------SE----SLVGGLIGRCGSNISRIRNESGAMIKVY 288 (330)
Q Consensus 219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~I------P~----~~vg~IIGk~G~~Ik~i~~~tga~I~i~ 288 (330)
..++...+-... +...-..+.| +. ..-|+|||++|.+.+.|++.|+|.|.|.
T Consensus 77 GF~pe~A~~LL~------------------d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~ 138 (194)
T COG1094 77 GFPPEKALKLLE------------------DDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY 138 (194)
T ss_pred CCCHHHHHHHhc------------------CCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe
Confidence 654322110000 0011111111 11 2459999999999999999999999999
Q ss_pred CCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 289 GGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 289 ~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
. ..|-|.|.+++++.|+..|.-+|..
T Consensus 139 g-------~tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 139 G-------KTVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred C-------cEEEEecChhhhHHHHHHHHHHHcC
Confidence 6 3699999999999999999877653
No 32
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=98.84 E-value=1.9e-09 Score=102.54 Aligned_cols=146 Identities=29% Similarity=0.373 Sum_probs=124.8
Q ss_pred cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (330)
Q Consensus 141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 220 (330)
..+..++.++...+-+++|+.|++|+.|+..+++++.+-.++ . .+++...+.|.+.++..|+..++.++.++
T Consensus 66 k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-------g~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 66 KDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-------GDERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred hheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-------CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence 456789999999999999999999999999999999986543 2 35677778889999999999999999876
Q ss_pred CCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEE
Q 020173 221 PPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQ 300 (330)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~ 300 (330)
. .+...+.+|...+++|+|++|++++.|+..++|+|.+..+...--.+...
T Consensus 138 ~-----------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~ 188 (608)
T KOG2279|consen 138 T-----------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIK 188 (608)
T ss_pred C-----------------------------cccccccchhhhcccccccchhhhcchhccccccccccccccccccccee
Confidence 2 35667889999999999999999999999999999999874333467888
Q ss_pred EEcCHHHHHHHHHHHHHHHHHHH
Q 020173 301 FGGSAQQVALAKQRVDEYIYSQL 323 (330)
Q Consensus 301 I~Gt~~~v~~A~~~I~~~i~~~~ 323 (330)
|.|...-++.|+.++.+.+++..
T Consensus 189 i~~qqk~~~~a~~~~~~~~~ede 211 (608)
T KOG2279|consen 189 ISGQQKEVAAAKHLILEKVSEDE 211 (608)
T ss_pred cccccchHHHHHhhhhccccchh
Confidence 89998888899999998877654
No 33
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.77 E-value=1.8e-08 Score=103.13 Aligned_cols=218 Identities=21% Similarity=0.272 Sum_probs=153.3
Q ss_pred CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCC
Q 020173 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDD 127 (330)
Q Consensus 48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~ 127 (330)
..+...+.+-..++..++||+|.+|.+|+++++|.|.++.. +..+..+.+.+.. .+..+|...+.....+...
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~-----~~~~ka~~~v~~~~~ei~n 417 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVS-----ANDEKAVEDVEKIIAEILN 417 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccc-----cchhHHHHHHHHHHHhhhc
Confidence 45778888899999999999999999999999999999984 4566778888875 4556666666666544432
Q ss_pred CCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhC-CeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH
Q 020173 128 SNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSG-ATIVILAPNQLPLCASAHESDRVVQISGDVPAV 206 (330)
Q Consensus 128 ~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sg-a~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v 206 (330)
. .....+++|...+..+||.+|..|..|..+++ ..|.+.... +.....++.|....+
T Consensus 418 ~-------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~---------~~~~~~~~~~~~~dv 475 (753)
T KOG2208|consen 418 S-------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN---------NSSDMVTIRGISKDV 475 (753)
T ss_pred c-------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC---------cccccceEecccccc
Confidence 1 12567899999999999999999999999999 555543221 233457788877777
Q ss_pred HHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEE
Q 020173 207 LNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIK 286 (330)
Q Consensus 207 ~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~ 286 (330)
..+...+..+........ .....+.....|..+.+..+|+.|..+. ..+....
T Consensus 476 ~~~~~~~~~~~~~a~~~~-----------------------~~~~~~~d~~~~~~~~~~~~g~~~~i~d----~~~~~~i 528 (753)
T KOG2208|consen 476 EKSVSLLKALKADAKNLK-----------------------FRDVVTKDKLLPVKYIGKEIGKNGTIRD----SLGDKSI 528 (753)
T ss_pred chhHHHHHhhhhhhhcch-----------------------hhhhhhccccchHHhhcccccCceeeec----cCCceee
Confidence 766555555554321100 0112344566667777777776665544 4455555
Q ss_pred EeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHH
Q 020173 287 VYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQ 322 (330)
Q Consensus 287 i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~ 322 (330)
++.. .+.++..++|.|..+.|..|...+..++...
T Consensus 529 ~~~~-~~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 529 FPPN-EDEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred cccc-cccccceeeecccccchhhhHHHHHhcchhh
Confidence 5542 2345678999999999999999888766543
No 34
>smart00322 KH K homology RNA-binding domain.
Probab=98.74 E-value=8.6e-08 Score=67.68 Aligned_cols=66 Identities=33% Similarity=0.462 Sum_probs=58.3
Q ss_pred eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (330)
Q Consensus 143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 217 (330)
.+.++.||...++.+||++|++|++|++.+|++|.+.... .....+.|.|+.+++..|..+|.+.+
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~---------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG---------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC---------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4789999999999999999999999999999999986421 14578999999999999999998876
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.58 E-value=8.4e-08 Score=85.52 Aligned_cols=154 Identities=17% Similarity=0.190 Sum_probs=114.6
Q ss_pred cceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhC
Q 020173 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLREN 220 (330)
Q Consensus 141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~ 220 (330)
..++..+.+|..+++.++|++|.+||.|+.+|..+|+-+... .+.++.++|..+.|..|+..|...-+..
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~----------eePiF~vTg~~edv~~aRrei~saaeH~ 93 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG----------EEPIFPVTGRHEDVRRARREIPSAAEHF 93 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC----------CCCcceeccCchhHHHHhhcCcccccee
Confidence 456888889999999999999999999999999999876543 4568999999999999999887633321
Q ss_pred CCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEE
Q 020173 221 PPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQ 300 (330)
Q Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~ 300 (330)
-. .-+.+.+..+... + +...+.+..+.+|...+|.+.|.+|.+|+.+++.++..|.-+-+ ..+-++-
T Consensus 94 ~l---~~~s~s~Sgg~~~----~---s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~---~~~~Vf~ 160 (394)
T KOG2113|consen 94 GL---IRASRSFSGGTNG----A---SASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR---CGEPVFC 160 (394)
T ss_pred ee---eeecccccCCCcc----c---cccCCCceeeeccceeeeeccccccCccchheecccceEeeecc---CCCceEE
Confidence 00 0111111111110 0 11345777889999999999999999999999999999988864 3567899
Q ss_pred EEcCHHH-HHHHH-HHHHH
Q 020173 301 FGGSAQQ-VALAK-QRVDE 317 (330)
Q Consensus 301 I~Gt~~~-v~~A~-~~I~~ 317 (330)
++|.+.+ +++|. ..|..
T Consensus 161 Vtg~~~nC~kra~s~eie~ 179 (394)
T KOG2113|consen 161 VTGAPKNCVKRARSCEIEQ 179 (394)
T ss_pred EecCCcchhhhccccchhh
Confidence 9999998 55555 34443
No 36
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.56 E-value=2e-07 Score=73.94 Aligned_cols=60 Identities=22% Similarity=0.429 Sum_probs=50.3
Q ss_pred ccccceecCCCchHHHHHHHhCCeEEEeCCCCC-----------------CceeEEEEEcC---HHHHHHHHHHHHHHHH
Q 020173 261 SLVGGLIGRCGSNISRIRNESGAMIKVYGGKGE-----------------QKHRHIQFGGS---AQQVALAKQRVDEYIY 320 (330)
Q Consensus 261 ~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~-----------------~~~r~v~I~Gt---~~~v~~A~~~I~~~i~ 320 (330)
+++|.|||.+|++||+|+++|||+|.|...... ...-.|.|++. .+.++.|..+|..++.
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 478999999999999999999999999975211 12357889995 5999999999998876
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.44 E-value=2.5e-07 Score=82.53 Aligned_cols=151 Identities=21% Similarity=0.312 Sum_probs=109.1
Q ss_pred CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc--
Q 020173 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD-- 125 (330)
Q Consensus 48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~-- 125 (330)
+.++..+.||..+++.|.|++|.+||.|+.+|+++|+-+.. ..+.++.++|.. ++|..|..+|..--.-.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~-----edv~~aRrei~saaeH~~l 95 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH-----EDVRRARREIPSAAEHFGL 95 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc-----hhHHHHhhcCccccceeee
Confidence 78999999999999999999999999999999999998875 356889999987 56677766665511000
Q ss_pred -CCCCcccccc-ccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCH
Q 020173 126 -DDSNSEASKV-AAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDV 203 (330)
Q Consensus 126 -~~~~~~~~~~-~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~ 203 (330)
.......... .+......+...-+|...+|++.|.+|.+|+.+++.++..|.-.-+ -.+.++.++|-+
T Consensus 96 ~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~----------~~~~Vf~Vtg~~ 165 (394)
T KOG2113|consen 96 IRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR----------CGEPVFCVTGAP 165 (394)
T ss_pred eeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc----------CCCceEEEecCC
Confidence 0000000000 1223445677888899999999999999999999999998876543 245688899988
Q ss_pred HH-HHHHH-HHHHHH
Q 020173 204 PA-VLNAL-VEIGNQ 216 (330)
Q Consensus 204 ~~-v~~A~-~~I~~~ 216 (330)
.+ +.+|. ..|+..
T Consensus 166 ~nC~kra~s~eie~t 180 (394)
T KOG2113|consen 166 KNCVKRARSCEIEQT 180 (394)
T ss_pred cchhhhccccchhhh
Confidence 88 44444 344443
No 38
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.42 E-value=6.3e-07 Score=71.04 Aligned_cols=71 Identities=20% Similarity=0.395 Sum_probs=50.8
Q ss_pred EEEecC------CccceeecccChhhhhhhhccCcEEEEecCCC---C--------------CcceEEEEecCCCCcchh
Q 020173 53 RIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADAIA---R--------------HEERVIIISSKDNDNVVS 109 (330)
Q Consensus 53 ~i~vP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~---~--------------~~ervi~I~G~~~~~~~~ 109 (330)
+|.||. +++|.|||++|.+||+|+++|||+|.|...-. + ...--|.|++.... .+
T Consensus 3 ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~--~e 80 (120)
T cd02395 3 KVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPP--EE 80 (120)
T ss_pred EEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcH--HH
Confidence 566776 57899999999999999999999999986410 0 01134777776410 15
Q ss_pred HHHHHHHHHHHHHhhc
Q 020173 110 DAENALQQIAALILKD 125 (330)
Q Consensus 110 ~~~~A~~~i~~~i~~~ 125 (330)
.+.+|+.+|..++...
T Consensus 81 ~~~~A~~~I~~ll~~~ 96 (120)
T cd02395 81 ALAKAVEAIEELLKPA 96 (120)
T ss_pred HHHHHHHHHHHHhccC
Confidence 6778888888877543
No 39
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.19 E-value=9.7e-06 Score=81.86 Aligned_cols=63 Identities=21% Similarity=0.352 Sum_probs=57.7
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY 320 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~ 320 (330)
....|.||.+.+|.|||.||.+||.|.++||++|.|.+ +..|.|.+. .+.+++|+.+|..++.
T Consensus 578 ~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d------~G~V~I~a~d~~~~~~A~~~I~~i~~ 641 (719)
T TIGR02696 578 RIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED------DGTVYIGAADGPSAEAARAMINAIAN 641 (719)
T ss_pred eeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec------CcEEEEEeCCHHHHHHHHHHHHHhhC
Confidence 67789999999999999999999999999999999995 367999885 8999999999998876
No 40
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.02 E-value=2.5e-05 Score=63.69 Aligned_cols=103 Identities=18% Similarity=0.305 Sum_probs=71.0
Q ss_pred eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (330)
Q Consensus 50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~ 129 (330)
-.+.++|+...+|+.||++|++|+.|++..|-+|.+-.-. + ++...+...+....-..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s-------------~---------d~~~fI~n~l~Pa~V~~ 89 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYS-------------D---------DPEEFIKNIFAPAAVRS 89 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcC-------------C---------CHHHHHHHHcCCCEEEE
Confidence 5678889999999999999999999999999888876521 1 12222333322111000
Q ss_pred ccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEE
Q 020173 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVI 178 (330)
Q Consensus 130 ~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i 178 (330)
. ... .........+.|+....|.+||++|++++.++.-++-.+.+
T Consensus 90 v---~I~-~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 90 V---TIK-KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred E---EEE-ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 0 000 00112356778999999999999999999999999877765
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.98 E-value=1.9e-05 Score=64.44 Aligned_cols=103 Identities=20% Similarity=0.269 Sum_probs=74.0
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~ 223 (330)
.+.++|+...+|..||++|++|+.|++..|-+|.+-.- +++ +..+|...+.-....
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~----------s~d--------------~~~fI~n~l~Pa~V~ 88 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY----------SDD--------------PEEFIKNIFAPAAVR 88 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc----------CCC--------------HHHHHHHHcCCCEEE
Confidence 68889999999999999999999999999988888632 121 233444444321110
Q ss_pred CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEe
Q 020173 224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY 288 (330)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~ 288 (330)
... .. .........+.|+.+..|..|||+|++++.++..++-.+.|.
T Consensus 89 ~v~-----I~-------------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 89 SVT-----IK-------------KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EEE-----EE-------------ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 000 00 011235667889999999999999999999999999988775
No 42
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.83 E-value=6.2e-05 Score=76.98 Aligned_cols=63 Identities=19% Similarity=0.265 Sum_probs=55.6
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY 320 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~ 320 (330)
....+.||.+.+|.|||++|++||.|.++|||+|.|.+ +..|.|.+. .+.++.|+++|..+..
T Consensus 551 ~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------dG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 551 RIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED------DGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec------CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 67789999999999999999999999999999999985 356777774 8899999999987754
No 43
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.65 E-value=0.00039 Score=66.20 Aligned_cols=72 Identities=24% Similarity=0.350 Sum_probs=56.3
Q ss_pred ceEEEEEEcc------ccccceecCCCchHHHHHHHhCCeEEEeCCC---------------C-CCceeEEEEEc-CHHH
Q 020173 251 YVTFEMLISE------SLVGGLIGRCGSNISRIRNESGAMIKVYGGK---------------G-EQKHRHIQFGG-SAQQ 307 (330)
Q Consensus 251 ~~~~~v~IP~------~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~---------------~-~~~~r~v~I~G-t~~~ 307 (330)
..+.+|.||- +|+|.|||..|.|.|+|+++|||+|.|-... . ..++=-+.|++ |.+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 3556677765 4899999999999999999999999998621 0 11223466777 5999
Q ss_pred HHHHHHHHHHHHHHH
Q 020173 308 VALAKQRVDEYIYSQ 322 (330)
Q Consensus 308 v~~A~~~I~~~i~~~ 322 (330)
|++|..+|+.+|.++
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999999863
No 44
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.58 E-value=0.00038 Score=56.69 Aligned_cols=103 Identities=18% Similarity=0.266 Sum_probs=68.8
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCc
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNS 130 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~ 130 (330)
.+-+.|....+|+.||++|++|+.|++..|=+|.+-.-. ... . .-+...+....-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys-----------~D~--------~---~fI~N~l~PA~V~-- 89 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYS-----------ENL--------E---EFVANKLAPAEVK-- 89 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcC-----------CCH--------H---HHHHHcCCCceEE--
Confidence 677889999999999999999999998889888876521 110 0 1111111100000
Q ss_pred cccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEe
Q 020173 131 EASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVIL 179 (330)
Q Consensus 131 ~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~ 179 (330)
.-.. ....+.....+.|+....+..||++|.+++..+.-++-++.+.
T Consensus 90 -~V~i-~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 90 -NVTV-SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred -EEEE-EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0000 0001223677889999999999999999999999988777653
No 45
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.58 E-value=0.0004 Score=70.44 Aligned_cols=94 Identities=24% Similarity=0.309 Sum_probs=70.9
Q ss_pred hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (330)
Q Consensus 108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~ 187 (330)
+..+.+++..|.+.+.+..... .. ....-+....+.||....+.|||++|.+||.|.++||++|.+.
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~~----~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-------- 614 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-DE----MSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-------- 614 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-cc----cccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe--------
Confidence 4455666667777665543322 11 1112244678899999999999999999999999999999995
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 219 (330)
++..|.|.+ +.+.+.+|+.+|..++..
T Consensus 615 -----d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 615 -----DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -----cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 345788877 688999999999999885
No 46
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.53 E-value=0.00021 Score=73.96 Aligned_cols=63 Identities=16% Similarity=0.247 Sum_probs=56.5
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCe-EEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAM-IKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY 320 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~-I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~ 320 (330)
....+.||.+.+|.|||.||.+||.|.++||+. |.+.+ +-.|.|.+. .+.++.|+.+|.++..
T Consensus 685 ~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d------dg~V~I~a~d~~~i~~A~~~I~~l~~ 749 (891)
T PLN00207 685 LIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD------DGTVKITAKDLSSLEKSKAIISSLTM 749 (891)
T ss_pred eeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC------CeeEEEEeCCHHHHHHHHHHHHHHhc
Confidence 677899999999999999999999999999999 88885 367888885 9999999999998864
No 47
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.47 E-value=0.0005 Score=56.01 Aligned_cols=103 Identities=17% Similarity=0.287 Sum_probs=71.4
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~ 223 (330)
.+-++|....+|..||++|++|+.|++..|-+|.+-. .+.++.. +|...+.-....
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVe------------------ys~D~~~------fI~N~l~PA~V~ 89 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIE------------------YSENLEE------FVANKLAPAEVK 89 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEE------------------cCCCHHH------HHHHcCCCceEE
Confidence 6778899999999999999999999998888887753 2222222 222222110000
Q ss_pred CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEe
Q 020173 224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY 288 (330)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~ 288 (330)
..... .........+.||.+..+..|||+|++++.....++-++.|.
T Consensus 90 ---~V~i~---------------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 90 ---NVTVS---------------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred ---EEEEE---------------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00000 001235677889999999999999999999999999888775
No 48
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.42 E-value=0.00031 Score=65.88 Aligned_cols=72 Identities=24% Similarity=0.275 Sum_probs=60.4
Q ss_pred ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHHH
Q 020173 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLIQ 325 (330)
Q Consensus 251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~~ 325 (330)
....-|.|-+++||.+||++|++|+.|+..|+++|+|.+. ..+-.|+|.|.-+--.+|+..|...+..+-..
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~m~~kaka~id~~~~k~e~y 117 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINHMRKKAKASIDRGQDKDERY 117 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHHHHHHHHhhHhhhhhhhhhc
Confidence 4566788999999999999999999999999999999973 45678999999888888888887766554433
No 49
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=97.38 E-value=0.00015 Score=64.15 Aligned_cols=41 Identities=24% Similarity=0.589 Sum_probs=36.9
Q ss_pred CCceEEEEEecCC------ccceeecccChhhhhhhhccCcEEEEec
Q 020173 47 AQDVLFRIIVPSR------QIGKVIGKEGHRIQKIREETKATIKIAD 87 (330)
Q Consensus 47 ~~~~~~~i~vP~~------~vg~IIGk~G~~Ik~I~~~tg~~I~i~~ 87 (330)
.-.++.+|+||.+ +||.|+|++|.++|+|+++|||+|.|.-
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrG 135 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRG 135 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEec
Confidence 3457889999985 8999999999999999999999999973
No 50
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.31 E-value=0.0017 Score=61.93 Aligned_cols=78 Identities=21% Similarity=0.262 Sum_probs=56.5
Q ss_pred ceEEEEEeec------cccceecCCCChhHHHHHHHhCCeEEEeCCCCCC---------cccCCCCCCcEEEEEcC-HHH
Q 020173 142 ANTIRLLIAG------SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP---------LCASAHESDRVVQISGD-VPA 205 (330)
Q Consensus 142 ~~~~~llip~------~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p---------~~~~~~~~~r~v~I~G~-~~~ 205 (330)
..+.+++||. .++|+|||..|.|.|+|+++|||+|.|-.+..+. .......++=-+.|+++ .+.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 3567888885 5789999999999999999999999997522111 11110122234677774 788
Q ss_pred HHHHHHHHHHHHhh
Q 020173 206 VLNALVEIGNQLRE 219 (330)
Q Consensus 206 v~~A~~~I~~~i~~ 219 (330)
|.+|++.|..+|.+
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 88899999999986
No 51
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.24 E-value=0.00047 Score=64.67 Aligned_cols=56 Identities=27% Similarity=0.446 Sum_probs=48.9
Q ss_pred CCCCceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCC
Q 020173 45 AKAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (330)
Q Consensus 45 ~~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~ 103 (330)
+...++.+++.|-+++||.+||++|++|+.|+..|+++|+|-.. ..+-.++|-|..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 34578999999999999999999999999999999999999875 456678888863
No 52
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=97.24 E-value=0.023 Score=49.64 Aligned_cols=129 Identities=15% Similarity=0.117 Sum_probs=97.7
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCC
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPR 223 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~ 223 (330)
.+.+.++....-++...+|..++.|....|++|.+.. ....+.|+|+...+..+...|...+...
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~------------~~~~i~I~g~k~~~~~i~~~i~~~l~~i--- 91 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR------------SENRIRITGTKSTAEYIEASINEILSNI--- 91 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec------------CCcEEEEEccHHHHHHHHHHHHHHHhhc---
Confidence 4566667888889999999999999888999999974 3568999999999999998888888754
Q ss_pred CCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceec----CCCchHHHHHHHhCCeEEEeCCCCCCceeEE
Q 020173 224 QVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIG----RCGSNISRIRNESGAMIKVYGGKGEQKHRHI 299 (330)
Q Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIG----k~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v 299 (330)
.+..|.++.-.--.--+ .....++.|++.|++.|...++ ...+
T Consensus 92 ----------------------------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~-----~~~~ 138 (210)
T PF14611_consen 92 ----------------------------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD-----GNKL 138 (210)
T ss_pred ----------------------------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC-----CCeE
Confidence 55566666443211111 2357899999999999998863 2234
Q ss_pred EEE-----cCHHHHHHHHHHHHHHHH
Q 020173 300 QFG-----GSAQQVALAKQRVDEYIY 320 (330)
Q Consensus 300 ~I~-----Gt~~~v~~A~~~I~~~i~ 320 (330)
.|+ -....++.|++++.-.+.
T Consensus 139 ~i~~~~~~~~~~~~~~a~RlL~~a~~ 164 (210)
T PF14611_consen 139 KISWLASPENEKRADRAKRLLLWALD 164 (210)
T ss_pred EEEEEeeccccchHHHHHHHHHHhcc
Confidence 444 468899999999987664
No 53
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.22 E-value=0.00092 Score=66.60 Aligned_cols=65 Identities=20% Similarity=0.308 Sum_probs=57.2
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQ 322 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~ 322 (330)
....+.|+.+.++.+||++|.+|++|.++||++|.+.++ -.|.|.++ .+.++.|+..|..+..+.
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idiedd------Gtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD------GTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecCC------CcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 567899999999999999999999999999999999942 45899897 588999999999887553
No 54
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.05 E-value=0.0023 Score=65.65 Aligned_cols=94 Identities=22% Similarity=0.192 Sum_probs=64.9
Q ss_pred hHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCccc
Q 020173 109 SDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCA 188 (330)
Q Consensus 109 ~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~ 188 (330)
..+.++...|.+.+.+........ ....-+....+.||...++.|||++|++||.|.++|||+|.|..
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~----~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-------- 588 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAE----LSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhcc----ccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec--------
Confidence 344555566666554432211100 01112346788899999999999999999999999999999952
Q ss_pred CCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173 189 SAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 189 ~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 219 (330)
+..|.|.+ ....+.+|...|..+...
T Consensus 589 -----dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 589 -----DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred -----CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 34566665 678888898888877653
No 55
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=97.03 E-value=0.00061 Score=62.02 Aligned_cols=71 Identities=34% Similarity=0.391 Sum_probs=57.5
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~ 125 (330)
+....+++++.+.|.|||++|.+.++|+++|+|+|.+|.+ ++....++|.|-. ...|..|..+|..+|...
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~----~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGIS----RNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehh----HHHHHHHHHHHHHHHHhh
Confidence 4667889999999999999999999999999999999987 3344456666643 467888888888887543
No 56
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.96 E-value=0.0053 Score=54.46 Aligned_cols=42 Identities=26% Similarity=0.514 Sum_probs=37.0
Q ss_pred CcceEEEEEEccc------cccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 249 ADYVTFEMLISES------LVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 249 ~~~~~~~v~IP~~------~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
....+.+|.||-. +||+|+|.+|.++|+|+++|||+|.|-..
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 3457788888865 99999999999999999999999999864
No 57
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.93 E-value=0.0013 Score=59.90 Aligned_cols=72 Identities=24% Similarity=0.265 Sum_probs=59.7
Q ss_pred ceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL 323 (330)
Q Consensus 251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~ 323 (330)
.+...+.++..+.|.|||++|.+.+.|+++|+++|.+|.+.+. .+.++.+.++-++|..|...|.-+|.+.-
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n-~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTN-KEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCCC-cceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 4667789999999999999999999999999999999986422 23344445579999999999998887764
No 58
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.92 E-value=0.00093 Score=46.38 Aligned_cols=37 Identities=30% Similarity=0.504 Sum_probs=34.2
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccCcEEEE
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i 85 (330)
.....+.||.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4678999999999999999999999999999988876
No 59
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.84 E-value=0.0029 Score=56.42 Aligned_cols=66 Identities=21% Similarity=0.220 Sum_probs=56.5
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHHHHHH
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIYSQLI 324 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~~~~~ 324 (330)
-+.+.||..+++.+||++|.+|+.|.+.+++.|.+.. +-.|-|+|+ .+.++.|+.+|..+-++.++
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~------NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ------NGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC------CcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 3678999999999999999999999999999999985 356888886 77999999999877665543
No 60
>PRK00106 hypothetical protein; Provisional
Probab=96.82 E-value=0.0067 Score=60.04 Aligned_cols=67 Identities=16% Similarity=0.335 Sum_probs=55.7
Q ss_pred cceEEEEEEccc-cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHH
Q 020173 250 DYVTFEMLISES-LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 250 ~~~~~~v~IP~~-~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~ 321 (330)
..+...|.+|++ +-|+|||+-|.+|+.+...||+.|-|.+ +...|+|+| .|---+.|+.-+..+|.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-----tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-----TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-----CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 446678899996 5599999999999999999999999995 234678999 588888888888777764
No 61
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=96.79 E-value=0.0067 Score=60.17 Aligned_cols=67 Identities=16% Similarity=0.320 Sum_probs=55.3
Q ss_pred cceEEEEEEccc-cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHH
Q 020173 250 DYVTFEMLISES-LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 250 ~~~~~~v~IP~~-~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~ 321 (330)
..+...|.+|++ +-|+|||+.|.+|+.+...||+.|-|.+ +...|+|+| .|---+.|+.-+..+|.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-----CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 346677899996 5599999999999999999999999995 234677998 488888888888777754
No 62
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.77 E-value=0.0051 Score=52.69 Aligned_cols=101 Identities=20% Similarity=0.248 Sum_probs=68.4
Q ss_pred EEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCC
Q 020173 146 RLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQV 225 (330)
Q Consensus 146 ~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~ 225 (330)
-+.+-...+|..||++|++++.|+++.|-+|.+-.- ++ ++ ...|...+. |- ..
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~----------s~--------d~------~~fI~nal~--Pa-~v 131 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW----------SE--------DP------AEFIKNALA--PA-EV 131 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe----------CC--------CH------HHHHHHhcC--cc-eE
Confidence 334445678999999999999999999977776532 11 11 123333332 10 00
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173 226 ISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG 289 (330)
Q Consensus 226 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~ 289 (330)
.++...+ .......+.||++..+..||++|.+++-..+.||-++.|..
T Consensus 132 ~~V~~~~----------------~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 132 LSVNIKE----------------DDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred eEEEEEe----------------CCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0110000 01126788899999999999999999999999999999985
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.76 E-value=0.0025 Score=65.53 Aligned_cols=63 Identities=21% Similarity=0.336 Sum_probs=54.1
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY 320 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~ 320 (330)
....+.||.+.++.+||.||.+||.|.++||+.|.+.+ +-.|.|.+. .+.++.|+++|..+..
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d------~G~v~i~~~~~~~~~~a~~~I~~~~~ 617 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED------DGTVKIAATDGEAAEAAKERIEGITA 617 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC------CceEEEEcccHHHHHHHHHHHHHhcc
Confidence 45567789999999999999999999999999888863 356888885 8999999999988764
No 64
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.70 E-value=0.0065 Score=52.04 Aligned_cols=102 Identities=22% Similarity=0.319 Sum_probs=67.3
Q ss_pred EEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcc
Q 020173 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSE 131 (330)
Q Consensus 52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~ 131 (330)
+-+.+-...+|..||++|.+|+.|.++.|=+|+|-.- +++. ..-+.+|+. . ....
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-------------s~d~--~~fI~nal~-------P---a~v~ 132 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-------------SEDP--AEFIKNALA-------P---AEVL 132 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-------------CCCH--HHHHHHhcC-------c---ceEe
Confidence 3444445678999999999999999999977776542 1110 112222221 0 0000
Q ss_pred ccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC
Q 020173 132 ASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (330)
Q Consensus 132 ~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~ 180 (330)
.-.. ... ......+.||....+..||++|.+++...+-||-++.|..
T Consensus 133 ~V~~-~~~-d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 133 SVNI-KED-DGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred EEEE-EeC-CCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 0000 000 1116788899999999999999999999999999999864
No 65
>PRK12704 phosphodiesterase; Provisional
Probab=96.68 E-value=0.0093 Score=59.26 Aligned_cols=67 Identities=15% Similarity=0.311 Sum_probs=53.5
Q ss_pred cceEEEEEEccc-cccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHH
Q 020173 250 DYVTFEMLISES-LVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 250 ~~~~~~v~IP~~-~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~ 321 (330)
..+...|.+|++ +-|+|||+.|.+||.+...||+.|-|.+ +...|.|+| .|-.-+.|+.-+..++.+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-----tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-----TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-----CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 346667889996 5599999999999999999999999995 235678999 477767777777666543
No 66
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.65 E-value=0.0032 Score=43.65 Aligned_cols=36 Identities=19% Similarity=0.351 Sum_probs=33.8
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEE
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV 287 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i 287 (330)
....+.||.+..|..|||+|.+|+.++..+|-+|.+
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 678899999999999999999999999999988876
No 67
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.50 E-value=0.0073 Score=62.87 Aligned_cols=95 Identities=17% Similarity=0.216 Sum_probs=67.5
Q ss_pred hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCe-EEEeCCCCCCc
Q 020173 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGAT-IVILAPNQLPL 186 (330)
Q Consensus 108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~-I~i~~~~~~p~ 186 (330)
+..+.+|+..|.+.+.+........ ....-.....+-||...++.|||.+|.+||.|.++||+. |.+.
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~----~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~------- 722 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKR----LSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ------- 722 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh----hcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-------
Confidence 3444555566666665543221110 111223467889999999999999999999999999999 8773
Q ss_pred ccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173 187 CASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 187 ~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 219 (330)
++-.|.|.+ +.+.+.+|+.+|..++.+
T Consensus 723 ------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 723 ------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 345677777 688999999999888864
No 68
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.45 E-value=0.0046 Score=52.67 Aligned_cols=43 Identities=21% Similarity=0.458 Sum_probs=37.3
Q ss_pred CCCceEEEEEecC------CccceeecccChhhhhhhhccCcEEEEecC
Q 020173 46 KAQDVLFRIIVPS------RQIGKVIGKEGHRIQKIREETKATIKIADA 88 (330)
Q Consensus 46 ~~~~~~~~i~vP~------~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (330)
....++-++.||. +++|+|||+.|.++|+|+..|+|+|-|.-.
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3456777888886 689999999999999999999999999754
No 69
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.34 E-value=0.012 Score=58.87 Aligned_cols=96 Identities=20% Similarity=0.204 Sum_probs=70.5
Q ss_pred hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (330)
Q Consensus 108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~ 187 (330)
+..+..|...|+..+.+........ ..........+-|+.....-+||++|.+|++|.+++|++|.+.
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~e----ls~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-------- 588 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKE----LSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-------- 588 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh----hhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec--------
Confidence 4556677777877776544322100 0111233667889999999999999999999999999999995
Q ss_pred cCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhC
Q 020173 188 ASAHESDRVVQISGD-VPAVLNALVEIGNQLREN 220 (330)
Q Consensus 188 ~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~ 220 (330)
++..|.|.++ .+.+.+|+..|..+.++-
T Consensus 589 -----ddGtv~i~~s~~~~~~~ak~~I~~i~~e~ 617 (692)
T COG1185 589 -----DDGTVKIAASDGESAKKAKERIEAITREV 617 (692)
T ss_pred -----CCCcEEEEecchHHHHHHHHHHHHHHhhc
Confidence 3456888876 588888999999998764
No 70
>PRK00468 hypothetical protein; Provisional
Probab=96.14 E-value=0.0051 Score=44.47 Aligned_cols=34 Identities=35% Similarity=0.587 Sum_probs=29.6
Q ss_pred CCCceEEEEEecCCccceeecccChhhhhhhhcc
Q 020173 46 KAQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (330)
Q Consensus 46 ~~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~t 79 (330)
.++.+.+++.+..+..|.||||+|.+++.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456889999999999999999999999998643
No 71
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.12 E-value=0.02 Score=53.78 Aligned_cols=95 Identities=23% Similarity=0.319 Sum_probs=63.3
Q ss_pred CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (330)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~ 137 (330)
+-+|+.||++|.+|+.|.++. |=+|+|-.-. + .+ ..-+.+|+.- .. -..+.-
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s---~--------d~----~~fi~nal~P-------a~-----v~~v~i 295 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS---D--------DP----AEFIANALSP-------AK-----VISVEV 295 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcC---C--------CH----HHHHHHhcCC-------ce-----EEEEEE
Confidence 459999999999999999998 7778775421 0 00 0111111110 00 000000
Q ss_pred CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC
Q 020173 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (330)
Q Consensus 138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~ 180 (330)
.........+.||..+.+..||++|.|++-...-||.+|.|..
T Consensus 296 ~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 296 LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0001136889999999999999999999999999999999975
No 72
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.04 E-value=0.017 Score=54.49 Aligned_cols=96 Identities=21% Similarity=0.194 Sum_probs=64.2
Q ss_pred CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (330)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~ 137 (330)
+-+|+.||++|.+|+.|.++. |=+|+|-.-. ++ -..-|...+.... -..+..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s-------------~D---------~~~fI~Nal~Pa~-----V~~V~i 303 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYS-------------NV---------PEIFIARALAPAI-----ISSVKI 303 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhCCCce-----eeEEEE
Confidence 458999999999999999988 7777775421 10 0001111111000 000000
Q ss_pred CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (330)
Q Consensus 138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~ 182 (330)
. .......+.||..+.+..||++|.+++-...-+|.+|.|..-+
T Consensus 304 ~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 304 E-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred c-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 0 1123678899999999999999999999999999999998644
No 73
>PRK02821 hypothetical protein; Provisional
Probab=95.98 E-value=0.0064 Score=44.12 Aligned_cols=35 Identities=26% Similarity=0.438 Sum_probs=30.1
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhccCc
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~ 81 (330)
.+.+.+++.+..+..|.||||+|.+++.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 45578999999999999999999999999965543
No 74
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.78 E-value=0.028 Score=53.10 Aligned_cols=96 Identities=23% Similarity=0.302 Sum_probs=64.0
Q ss_pred CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (330)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~ 137 (330)
+-+|+.||++|.+|+.|.++. |=+|+|-.-. + +-...|...+.... -..+.-
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s-------------~---------d~~~fi~nal~Pa~-----v~~v~i 297 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWS-------------E---------DPAEFVANALSPAK-----VVSVEV 297 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcC-------------C---------CHHHHHHHhCCCce-----EEEEEE
Confidence 459999999999999999888 7888875421 1 00011111111000 000000
Q ss_pred CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (330)
Q Consensus 138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~ 181 (330)
.........+.||..+.+..||++|.|++-...-+|.+|.|...
T Consensus 298 ~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 298 DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00112368899999999999999999999999999999999754
No 75
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.72 E-value=0.024 Score=53.40 Aligned_cols=95 Identities=17% Similarity=0.168 Sum_probs=65.0
Q ss_pred ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCC
Q 020173 153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA 231 (330)
Q Consensus 153 ~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~ 231 (330)
-+|..||.+|++|+.|.++. |-+|.+-.- +++. ..+|...|.-. ...++.
T Consensus 252 PvGacIG~~G~rI~~I~~eL~gEkIDvI~~----------s~D~--------------~~fI~Nal~Pa---~V~~V~-- 302 (374)
T PRK12328 252 PIGATVGVKGVRINAVSKELNGENIDCIEY----------SNVP--------------EIFIARALAPA---IISSVK-- 302 (374)
T ss_pred hHHhhcCCCcchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhCCCc---eeeEEE--
Confidence 47999999999999998887 777877642 1221 11222222100 000000
Q ss_pred CCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC
Q 020173 232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK 291 (330)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~ 291 (330)
-........+.||.+..+.-|||+|++++-....||.+|.|..-.
T Consensus 303 ---------------i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 303 ---------------IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred ---------------EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 001235678999999999999999999999999999999998653
No 76
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.63 E-value=0.025 Score=58.30 Aligned_cols=95 Identities=21% Similarity=0.202 Sum_probs=66.1
Q ss_pred hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (330)
Q Consensus 108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~ 187 (330)
+..+.+++..|.+.+.+......... .........+.|+...++.+||.+|.+||.|.+++|+.|.+.
T Consensus 523 l~~a~~g~~~I~~~M~~aI~~~r~~~----~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-------- 590 (693)
T PRK11824 523 LEQAKEGRLHILGKMNEAISEPRAEL----SPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-------- 590 (693)
T ss_pred HHHHHHHHHHHHHHHHHHhcCChhhh----cccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC--------
Confidence 34556666777777765433221111 011123456667889999999999999999999999988763
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 219 (330)
++..|.|.+ ..+.+.+|...|..+..+
T Consensus 591 -----d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 591 -----DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred -----CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 345677777 688888899988887754
No 77
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.61 E-value=0.026 Score=48.18 Aligned_cols=40 Identities=28% Similarity=0.402 Sum_probs=33.9
Q ss_pred eEEEEEee------ccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173 143 NTIRLLIA------GSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (330)
Q Consensus 143 ~~~~llip------~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~ 182 (330)
++-+++|| ..++|+|||+.|+++|+|++.|+|+|.|-...
T Consensus 148 ~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 148 YQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 45677777 45799999999999999999999999996543
No 78
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.56 E-value=0.031 Score=54.74 Aligned_cols=92 Identities=24% Similarity=0.379 Sum_probs=63.2
Q ss_pred ccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHH--HHHHHhhcCCCCccccccc
Q 020173 60 QIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQ--IAALILKDDDSNSEASKVA 136 (330)
Q Consensus 60 ~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~--i~~~i~~~~~~~~~~~~~~ 136 (330)
-+|+.||++|.+|+.|.++. |=+|+|-.-. ++. ..-+.+|+.- +..++.+.
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s---~d~------------~~fi~nal~pa~v~~v~~~~----------- 299 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWS---DDP------------AQFIINALSPAEVSSVVVDE----------- 299 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcC---CCH------------HHHHHHhCCCCEEEEEEEeC-----------
Confidence 48999999999999999988 7788875421 100 0111111100 00000000
Q ss_pred cCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173 137 AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (330)
Q Consensus 137 ~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~ 181 (330)
......+.||..+.+..||++|.|++..+.-+|.+|.|...
T Consensus 300 ----~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 300 ----DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred ----CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 11278899999999999999999999999999999999753
No 79
>PRK01064 hypothetical protein; Provisional
Probab=95.50 E-value=0.015 Score=42.33 Aligned_cols=33 Identities=36% Similarity=0.708 Sum_probs=29.4
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhcc
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREET 79 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~t 79 (330)
...+.+++.|.....|.+|||+|.+|+.|+.-.
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 456889999999999999999999999999643
No 80
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.44 E-value=0.032 Score=54.53 Aligned_cols=69 Identities=25% Similarity=0.228 Sum_probs=56.8
Q ss_pred cceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEc-CHHHHHHHHHHHHHHHHHHHHH
Q 020173 250 DYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGG-SAQQVALAKQRVDEYIYSQLIQ 325 (330)
Q Consensus 250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~G-t~~~v~~A~~~I~~~i~~~~~~ 325 (330)
......+.++++....+||.+|.+.|.|..+||+.-.+. +..++|.. ++...+.|+.+|..++-...++
T Consensus 595 ~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD-------e~t~~i~A~~~~am~~Ak~~I~~i~~~~~~~ 664 (760)
T KOG1067|consen 595 SPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD-------EGTFSIFAPTQAAMEEAKEFIDGIIKDDQVQ 664 (760)
T ss_pred CceeeEEeecchhhheeecCccceeeeEeeeccceeeec-------CceEEEEecCHHHHHHHHHHHHHHhcCcccc
Confidence 346778999999999999999999999999999655554 35688877 5999999999999887664443
No 81
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.44 E-value=0.031 Score=53.63 Aligned_cols=95 Identities=23% Similarity=0.277 Sum_probs=62.7
Q ss_pred CccceeecccChhhhhhhhcc-CcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCcccccccc
Q 020173 59 RQIGKVIGKEGHRIQKIREET-KATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAA 137 (330)
Q Consensus 59 ~~vg~IIGk~G~~Ik~I~~~t-g~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~ 137 (330)
+-+|+.||++|.+|+.|.++. |=+|+|-.-. ++ -...|...+.... -..+.-
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-------------~D---------p~~fI~NaLsPA~-----V~~V~i 329 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-------------PD---------PATYIANALSPAR-----VDEVRL 329 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-------------CC---------HHHHHHHhcCCce-----eeEEEE
Confidence 459999999999999999998 7777775421 10 0001111110000 000000
Q ss_pred CCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC
Q 020173 138 GHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA 180 (330)
Q Consensus 138 ~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~ 180 (330)
.........+.||..+.++.||++|.|++-...-||.+|.|..
T Consensus 330 ~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 330 VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0001135789999999999999999999999999999999864
No 82
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.42 E-value=0.016 Score=41.85 Aligned_cols=32 Identities=41% Similarity=0.637 Sum_probs=28.6
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhc
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREE 78 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~ 78 (330)
...+.+++-+.....|.||||+|.+|+.|+.-
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 45678999999999999999999999999854
No 83
>PRK12705 hypothetical protein; Provisional
Probab=95.36 E-value=0.045 Score=53.97 Aligned_cols=66 Identities=17% Similarity=0.262 Sum_probs=48.7
Q ss_pred cceEEEEEEccccc-cceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcC-HHHHHHHHHHHHHHHH
Q 020173 250 DYVTFEMLISESLV-GGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGS-AQQVALAKQRVDEYIY 320 (330)
Q Consensus 250 ~~~~~~v~IP~~~v-g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt-~~~v~~A~~~I~~~i~ 320 (330)
......+.+|++-. |+|||+-|.+|+.+...||+.|.|.+. ...|+|++- |.--+.|...+..+|.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt-----p~~V~ls~fdp~rreia~~~l~~Li~ 263 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT-----PEAVVISSFNPIRREIARLTLEKLLA 263 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC-----ccchhhcccCccchHHHHHHHHHHHh
Confidence 34666788998755 999999999999999999999999963 234666664 5555555555555543
No 84
>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=95.31 E-value=0.05 Score=51.10 Aligned_cols=94 Identities=24% Similarity=0.312 Sum_probs=63.9
Q ss_pred ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCC
Q 020173 153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA 231 (330)
Q Consensus 153 ~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~ 231 (330)
-+|..||.+|++|+.|.++. |-+|.+-.- +++. ..+|...|.-... .++
T Consensus 244 pvga~vG~~G~ri~~i~~el~ge~Idiv~~----------s~d~--------------~~fi~nal~Pa~v---~~v--- 293 (341)
T TIGR01953 244 PVGACVGPKGSRIQAISKELNGEKIDIIEY----------SDDP--------------AEFIANALSPAKV---ISV--- 293 (341)
T ss_pred cceeeECCCCchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhcCCceE---EEE---
Confidence 37999999999999999887 777777642 2221 1122222210000 000
Q ss_pred CCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173 232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG 289 (330)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~ 289 (330)
.. .........+.||.+..+.-|||+|.+++-....||.+|.|..
T Consensus 294 -----------~i--~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 294 -----------EV--LDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred -----------EE--EcCCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 00 0012257889999999999999999999999999999999975
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.16 E-value=0.043 Score=53.74 Aligned_cols=103 Identities=20% Similarity=0.304 Sum_probs=68.8
Q ss_pred EEEEEeecc-----ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173 144 TIRLLIAGS-----QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (330)
Q Consensus 144 ~~~llip~~-----~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 217 (330)
..++.|-+. -+|..||.+|++|+.|.++. |-+|.+..- +++. ..+|...|
T Consensus 232 RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~----------s~d~--------------~~fi~nal 287 (470)
T PRK09202 232 RAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILW----------SDDP--------------AQFIINAL 287 (470)
T ss_pred eeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhC
Confidence 345555432 37999999999999999887 777777642 2221 11222222
Q ss_pred hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
.-.... .+. -........+.||.+..+.-|||+|++++-....||.+|.|...
T Consensus 288 ~pa~v~---~v~-----------------~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 288 SPAEVS---SVV-----------------VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CCCEEE---EEE-----------------EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 110000 000 00112578899999999999999999999999999999999863
No 86
>PRK00468 hypothetical protein; Provisional
Probab=95.15 E-value=0.027 Score=40.70 Aligned_cols=32 Identities=25% Similarity=0.380 Sum_probs=28.2
Q ss_pred cceEEEEEEccccccceecCCCchHHHHHHHh
Q 020173 250 DYVTFEMLISESLVGGLIGRCGSNISRIRNES 281 (330)
Q Consensus 250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t 281 (330)
....+++.+.++-+|+||||+|.+|+.|+.--
T Consensus 28 ~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 28 QSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 34778899999999999999999999998764
No 87
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.10 E-value=0.06 Score=50.95 Aligned_cols=95 Identities=19% Similarity=0.262 Sum_probs=64.7
Q ss_pred ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCC
Q 020173 153 QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPA 231 (330)
Q Consensus 153 ~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~ 231 (330)
-+|..||++|++|+.|.++. |-+|.+-.- +++. ..+|...|.-... .++
T Consensus 246 pvGa~iG~~G~rI~~i~~el~gekIdiv~~----------s~d~--------------~~fi~nal~Pa~v---~~v--- 295 (362)
T PRK12327 246 AKGACVGPKGQRVQNIVSELKGEKIDIIDW----------SEDP--------------AEFVANALSPAKV---VSV--- 295 (362)
T ss_pred chheeECCCChhHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhCCCceE---EEE---
Confidence 47999999999999998887 777777642 2221 1122222210000 000
Q ss_pred CCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 232 YNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 232 ~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
.-.........+.||.+..+.-|||+|.+++-....||.+|.|...
T Consensus 296 -------------~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 296 -------------EVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred -------------EEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 0000123568899999999999999999999999999999999864
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.01 E-value=0.061 Score=47.94 Aligned_cols=65 Identities=22% Similarity=0.227 Sum_probs=53.2
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC-HHHHHHHHHHHHHHHhhCC
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD-VPAVLNALVEIGNQLRENP 221 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~i~~~~ 221 (330)
-+.+-||...++.+||++|.+|+.|.+.+++.|.+- .+..|.|.+. .+++.+|..+|..+-++..
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-------------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~ 211 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-------------QNGRIWIKGPDEEDEEIAIEAIKKIEREAH 211 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-------------CCcEEEEeeCCHHHHHHHHHHHHHHHhhhh
Confidence 356889999999999999999999999999999883 3456888886 5578888888877776653
No 89
>PRK02821 hypothetical protein; Provisional
Probab=94.98 E-value=0.031 Score=40.59 Aligned_cols=33 Identities=27% Similarity=0.383 Sum_probs=28.9
Q ss_pred ceEEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGA 283 (330)
Q Consensus 251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga 283 (330)
...+.+.+.++-+|+||||+|.+|+.|+.--.+
T Consensus 30 ~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 30 GRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred cEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 367899999999999999999999999887543
No 90
>PRK12704 phosphodiesterase; Provisional
Probab=94.91 E-value=0.048 Score=54.24 Aligned_cols=51 Identities=25% Similarity=0.484 Sum_probs=42.2
Q ss_pred CceEEEEEecC-CccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCC
Q 020173 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKD 103 (330)
Q Consensus 48 ~~~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~ 103 (330)
...+-.+.+|+ +.-|.||||.|.||+.++.-||+.|-|++. + .+|+++|-+
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----p-~~v~ls~~~ 259 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----P-EAVILSGFD 259 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----C-CeEEEecCC
Confidence 34566778898 569999999999999999999999999874 3 457788853
No 91
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.83 E-value=0.065 Score=51.47 Aligned_cols=103 Identities=18% Similarity=0.260 Sum_probs=67.7
Q ss_pred EEEEEeecc-----ccceecCCCChhHHHHHHHh-CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHH
Q 020173 144 TIRLLIAGS-----QAGCLIGMSGQNIEKLRNSS-GATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQL 217 (330)
Q Consensus 144 ~~~llip~~-----~~g~iIG~~G~~Ik~I~~~s-ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i 217 (330)
..++.|-+. -+|..||.+|++|+.|.++. |-+|.+..- +++. ..+|...|
T Consensus 264 RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~y----------s~Dp--------------~~fI~NaL 319 (449)
T PRK12329 264 RTKIAVDTLERDVDPVGACIGARGSRIQAVVNELRGEKIDVIRW----------SPDP--------------ATYIANAL 319 (449)
T ss_pred eeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEEc----------CCCH--------------HHHHHHhc
Confidence 445555432 37999999999999999887 777777542 1221 11222222
Q ss_pred hhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeC
Q 020173 218 RENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYG 289 (330)
Q Consensus 218 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~ 289 (330)
.-.... ++. . .........+.||.+..+.-|||+|.+++-....||.+|.|..
T Consensus 320 sPA~V~---~V~--------------i--~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 320 SPARVD---EVR--------------L--VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred CCceee---EEE--------------E--EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 100000 000 0 0012245789999999999999999999999999999999985
No 92
>PRK00106 hypothetical protein; Provisional
Probab=94.66 E-value=0.11 Score=51.50 Aligned_cols=64 Identities=23% Similarity=0.375 Sum_probs=48.9
Q ss_pred EEEEEeec-cccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173 144 TIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 144 ~~~llip~-~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 219 (330)
...+.+|+ .+-|+|||+.|.||+.|+.-||+.+-|.. +...|+|+| +|---.-|...+..++.+
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd------------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD------------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC------------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 45667787 57799999999999999999999999852 334677888 565555566666666654
No 93
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.63 E-value=0.11 Score=51.68 Aligned_cols=64 Identities=22% Similarity=0.332 Sum_probs=48.3
Q ss_pred EEEEEeec-cccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhh
Q 020173 144 TIRLLIAG-SQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISG-DVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 144 ~~~llip~-~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~ 219 (330)
...+.+|+ .+-|+|||+.|.||+.|+..||+.+-|.. +...|+|+| +|---.-|...+..++.+
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 45667777 57799999999999999999999999852 334677888 455555566666666654
No 94
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.54 E-value=1.9 Score=37.47 Aligned_cols=130 Identities=15% Similarity=0.119 Sum_probs=83.2
Q ss_pred EEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccc
Q 020173 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEA 132 (330)
Q Consensus 53 ~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~ 132 (330)
.+.++....-++...+|..++.|-...||+|.+.. ++..+.|+|++ ..+..+...|.+.+..-
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k-----~~~~~i~~~i~~~l~~i------- 91 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTK-----STAEYIEASINEILSNI------- 91 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccH-----HHHHHHHHHHHHHHhhc-------
Confidence 34445778889999999999999888899999986 35679999986 23333333344433211
Q ss_pred cccccCCCcceEEEEEeeccccceec-C---CCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEE-----cCH
Q 020173 133 SKVAAGHVAANTIRLLIAGSQAGCLI-G---MSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQIS-----GDV 203 (330)
Q Consensus 133 ~~~~~~~~~~~~~~llip~~~~g~iI-G---~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~-----G~~ 203 (330)
.+..+-++.-....-. + .....++.|++.|++.+..... +..+.|. -..
T Consensus 92 ----------~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~------------~~~~~i~~~~~~~~~ 149 (210)
T PF14611_consen 92 ----------RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD------------GNKLKISWLASPENE 149 (210)
T ss_pred ----------EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC------------CCeEEEEEEeecccc
Confidence 1333333322111111 1 1345689999999999997642 2234443 467
Q ss_pred HHHHHHHHHHHHHHhhCC
Q 020173 204 PAVLNALVEIGNQLRENP 221 (330)
Q Consensus 204 ~~v~~A~~~I~~~i~~~~ 221 (330)
..+..|..++...+...+
T Consensus 150 ~~~~~a~RlL~~a~~~~~ 167 (210)
T PF14611_consen 150 KRADRAKRLLLWALDYNP 167 (210)
T ss_pred chHHHHHHHHHHhccCCc
Confidence 788888988888885443
No 95
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=94.07 E-value=0.0093 Score=62.41 Aligned_cols=72 Identities=19% Similarity=0.117 Sum_probs=61.6
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC-CCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHHH
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG-KGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQLI 324 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~-~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~~ 324 (330)
.-++.+|-....+|||++|.+|+.++..||+.|.+.+- .+...+|.+.+.|.++.+..|-..|.-.|.+..+
T Consensus 1341 ~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~I~~~i~Dpdv 1413 (2131)
T KOG4369|consen 1341 QGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSPIGLPIIDPDV 1413 (2131)
T ss_pred ccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhccccceeecCCc
Confidence 45788999999999999999999999999999999983 3345699999999999999999888877765443
No 96
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.03 E-value=0.069 Score=38.53 Aligned_cols=32 Identities=31% Similarity=0.456 Sum_probs=28.2
Q ss_pred cceEEEEEeeccccceecCCCChhHHHHHHHh
Q 020173 141 AANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS 172 (330)
Q Consensus 141 ~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~s 172 (330)
....+++.+.....|.+||++|.+|+.|+.--
T Consensus 28 ~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 45578999999999999999999999999753
No 97
>PRK01064 hypothetical protein; Provisional
Probab=93.69 E-value=0.088 Score=38.33 Aligned_cols=32 Identities=25% Similarity=0.515 Sum_probs=28.2
Q ss_pred cceEEEEEEccccccceecCCCchHHHHHHHh
Q 020173 250 DYVTFEMLISESLVGGLIGRCGSNISRIRNES 281 (330)
Q Consensus 250 ~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t 281 (330)
....+++.+..+-.|.+|||+|.+|+.|+.-.
T Consensus 28 ~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 28 HTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred CEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 44778899999999999999999999998753
No 98
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=93.39 E-value=0.23 Score=42.35 Aligned_cols=155 Identities=17% Similarity=0.150 Sum_probs=92.2
Q ss_pred eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (330)
Q Consensus 50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~ 129 (330)
-+-++.||.....-+=-.==..-.-|-+..+.+|.+.-. .|-+.+.-..+.....+.+++..-+..++...+...
T Consensus 74 e~Rkvpvpp~r~tplk~~W~kIytPive~lklqiRmNlK-----~r~VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~D 148 (252)
T KOG3273|consen 74 ETRKVPVPPHRYTPLKDNWMKIYTPIVEHLKLQIRMNLK-----ARSVELRTCKDTEDPSALQKGADFVRAFILGFDIDD 148 (252)
T ss_pred ceeeccCCcccCChHHHhhHhhhhHHHHhhhheeEeecc-----cceeEeecCCCCCChHHHHHHHHHHHHHHhCCcchh
Confidence 345677777655332100001112255677777777643 244444433333234666777777777766554322
Q ss_pred ccc------cccc-cCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcC
Q 020173 130 SEA------SKVA-AGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGD 202 (330)
Q Consensus 130 ~~~------~~~~-~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~ 202 (330)
.-. .... ..-....+++=.=-+..+|+|+|++|.+--.|++.|-++|.+. +..|.|-|.
T Consensus 149 AiALlrlddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVla--------------d~kIHiLG~ 214 (252)
T KOG3273|consen 149 AIALLRLDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLA--------------DSKIHILGA 214 (252)
T ss_pred HHHHHhhhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEec--------------CceEEEeec
Confidence 100 0000 0000001111111245679999999999889999999999884 347999999
Q ss_pred HHHHHHHHHHHHHHHhhCCCC
Q 020173 203 VPAVLNALVEIGNQLRENPPR 223 (330)
Q Consensus 203 ~~~v~~A~~~I~~~i~~~~~~ 223 (330)
.+++.-|+..|+.+|-.+|+.
T Consensus 215 ~~niriAR~avcsLIlGsppg 235 (252)
T KOG3273|consen 215 FQNIRIARDAVCSLILGSPPG 235 (252)
T ss_pred chhhHHHHHhhHhhhccCCch
Confidence 999999999999999888654
No 99
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.31 E-value=0.036 Score=39.77 Aligned_cols=35 Identities=17% Similarity=0.352 Sum_probs=29.5
Q ss_pred CCceEEEEEecCCccceeecccChhhhhhhhccCc
Q 020173 47 AQDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (330)
Q Consensus 47 ~~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~ 81 (330)
.+...+.+.+..+..|.+|||+|.+++.||.-.+.
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 35667888889999999999999999999966553
No 100
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=92.70 E-value=0.15 Score=35.31 Aligned_cols=35 Identities=29% Similarity=0.462 Sum_probs=28.3
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccCcEE
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I 83 (330)
.....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45556666666799999999999999999988544
No 101
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=91.90 E-value=0.09 Score=37.67 Aligned_cols=33 Identities=24% Similarity=0.275 Sum_probs=28.7
Q ss_pred ceEEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173 251 YVTFEMLISESLVGGLIGRCGSNISRIRNESGA 283 (330)
Q Consensus 251 ~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga 283 (330)
...+.+.+..+..|.+|||+|.+++.|+.-.+.
T Consensus 28 ~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 28 GDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred ceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 467888899999999999999999999876654
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=91.43 E-value=0.22 Score=35.41 Aligned_cols=38 Identities=32% Similarity=0.392 Sum_probs=30.1
Q ss_pred EEEEEEcccc-----ccceecCCCchHHHHHHHh-CCeEEEeCC
Q 020173 253 TFEMLISESL-----VGGLIGRCGSNISRIRNES-GAMIKVYGG 290 (330)
Q Consensus 253 ~~~v~IP~~~-----vg~IIGk~G~~Ik~i~~~t-ga~I~i~~~ 290 (330)
...+.|-... +|..||.+|++|+.|.++. |-+|.+-..
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 4566777776 8999999999999999999 889988764
No 103
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=91.25 E-value=0.14 Score=43.51 Aligned_cols=122 Identities=16% Similarity=0.130 Sum_probs=80.5
Q ss_pred HHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCC
Q 020173 168 LRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPT 247 (330)
Q Consensus 168 I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (330)
|-+..+.+|.++-+... -+-|...-+-++.+++++...|.+.+...+..+.+... +
T Consensus 99 ive~lklqiRmNlK~r~-------VelRt~~~t~D~s~Lqk~adfv~Af~lGF~i~DAiALl--------r--------- 154 (252)
T KOG3273|consen 99 IVEHLKLQIRMNLKARS-------VELRTCKDTEDPSALQKGADFVRAFILGFDIDDAIALL--------R--------- 154 (252)
T ss_pred HHHhhhheeEeecccce-------eEeecCCCCCChHHHHHHHHHHHHHHhCCcchhHHHHH--------h---------
Confidence 56777877877643110 11222333456889999999998888765432211000 0
Q ss_pred CCcceEEEEEE----------ccccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHH
Q 020173 248 SADYVTFEMLI----------SESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDE 317 (330)
Q Consensus 248 ~~~~~~~~v~I----------P~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~ 317 (330)
....+...|.| -...+|+|+|++|.+--.|++.|.++|.+.+ ..|.|-|+.+++..|+..|-.
T Consensus 155 lddlflesFEi~dVKtL~GdHlsRAIGRiaGk~GkTkfaIEn~trtrIVlad-------~kIHiLG~~~niriAR~avcs 227 (252)
T KOG3273|consen 155 LDDLFLESFEIKDVKTLKGDHLSRAIGRIAGKGGKTKFAIENVTRTRIVLAD-------SKIHILGAFQNIRIARDAVCS 227 (252)
T ss_pred hhhhhheeeeecccccccchhHHHHHHHhhcCCCcceeeeeccceeEEEecC-------ceEEEeecchhhHHHHHhhHh
Confidence 00011112222 2347899999999999999999999999985 358999999999999998877
Q ss_pred HHH
Q 020173 318 YIY 320 (330)
Q Consensus 318 ~i~ 320 (330)
+|.
T Consensus 228 LIl 230 (252)
T KOG3273|consen 228 LIL 230 (252)
T ss_pred hhc
Confidence 764
No 104
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=91.08 E-value=0.69 Score=45.59 Aligned_cols=95 Identities=20% Similarity=0.199 Sum_probs=67.3
Q ss_pred hhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcc
Q 020173 108 VSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLC 187 (330)
Q Consensus 108 ~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~ 187 (330)
+.++.+|...|++.+.+...... ............+-++.+....+||++|...|+|..+||+.-.+
T Consensus 566 l~~a~~ar~~Il~~m~k~i~~Pr----~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v--------- 632 (760)
T KOG1067|consen 566 LQKAREARLQILDIMEKNINSPR----GSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV--------- 632 (760)
T ss_pred HHhhhHHHHHHHHHHHhhcCCcc----cCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------
Confidence 34556666777877765543221 11222344577888999999999999999999999999953333
Q ss_pred cCCCCCCcEEEEEc-CHHHHHHHHHHHHHHHhhC
Q 020173 188 ASAHESDRVVQISG-DVPAVLNALVEIGNQLREN 220 (330)
Q Consensus 188 ~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~i~~~ 220 (330)
++..+.|-. +.....+|++.|..++...
T Consensus 633 -----De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 633 -----DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred -----cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 345677666 5778888999998888764
No 105
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=90.90 E-value=0.49 Score=45.99 Aligned_cols=154 Identities=14% Similarity=0.157 Sum_probs=108.0
Q ss_pred eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCC
Q 020173 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSN 129 (330)
Q Consensus 50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~ 129 (330)
..+.+.||.+.+..|||.||..|.+++...++.|.+.... ++ | .+ . + .+
T Consensus 449 ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~----~~-----~-------qs----------~-~-~d--- 497 (657)
T COG5166 449 AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFY----KF-----G-------QS----------Q-W-HD--- 497 (657)
T ss_pred hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhh----hc-----c-------hh----------h-h-hc---
Confidence 3567889999999999999999999999999888886531 00 1 00 0 0 00
Q ss_pred ccccccccCCCcceEEEEEeeccccceecCCCChhHHHHHHHh----CCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHH
Q 020173 130 SEASKVAAGHVAANTIRLLIAGSQAGCLIGMSGQNIEKLRNSS----GATIVILAPNQLPLCASAHESDRVVQISGDVPA 205 (330)
Q Consensus 130 ~~~~~~~~~~~~~~~~~llip~~~~g~iIG~~G~~Ik~I~~~s----ga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~ 205 (330)
.+-+-.|.+-.+.|+|++.-.+..+++.+ ...|.+.. ..-+++++-|-.+.
T Consensus 498 --------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~-----------~~~sI~~v~~~~~~ 552 (657)
T COG5166 498 --------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP-----------QSTSIFTVDIYSDE 552 (657)
T ss_pred --------------ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC-----------CceEEEEEcccccH
Confidence 24566788888999999988887787665 34555542 24568999998877
Q ss_pred HHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceec---CCCchHHHHHHHhC
Q 020173 206 VLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIG---RCGSNISRIRNESG 282 (330)
Q Consensus 206 v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIG---k~G~~Ik~i~~~tg 282 (330)
+.+... -...+.+. .....+.+|.+.++..+| -.|++|..+.....
T Consensus 553 I~rv~k-ne~v~~~~------------------------------p~~~~~y~~se~h~~g~gena~R~~ni~~~t~~y~ 601 (657)
T COG5166 553 IERVIK-NETVLLEF------------------------------PAEMHFYVPSEIHKKGIGENAFRGENIQRVTKLYN 601 (657)
T ss_pred HHHHhh-ccceEEec------------------------------ccccccccchhhhhccCCcccccccchhhhhhhhh
Confidence 665443 22222222 133457889999999999 78999999988888
Q ss_pred CeEEEeCC
Q 020173 283 AMIKVYGG 290 (330)
Q Consensus 283 a~I~i~~~ 290 (330)
-.|...-.
T Consensus 602 ~~ie~~~t 609 (657)
T COG5166 602 SYIEFSTT 609 (657)
T ss_pred ccceeecC
Confidence 88877754
No 106
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=90.54 E-value=1.3 Score=36.05 Aligned_cols=90 Identities=26% Similarity=0.229 Sum_probs=60.4
Q ss_pred CCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHH---HHHHHHHHHHHhhCCCCCCcccCCCCCCC
Q 020173 159 GMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAV---LNALVEIGNQLRENPPRQVISISPAYNYS 235 (330)
Q Consensus 159 G~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v---~~A~~~I~~~i~~~~~~~~~~~~~~~~~~ 235 (330)
-.+|.-|++|...---+|.+- .+++.. ..|.+.|.+++-++-.- .++.
T Consensus 22 ~~~~dli~~lAk~lrKRIvvR---------------------~dps~l~~~e~A~~~I~~ivP~ea~i------~di~-- 72 (145)
T cd02410 22 AEDGDLVKDLAKDLRKRIVIR---------------------PDPSVLKPPEEAIKIILEIVPEEAGI------TDIY-- 72 (145)
T ss_pred hcccHHHHHHHHHHhceEEEc---------------------CChhhcCCHHHHHHHHHHhCCCccCc------eeeE--
Confidence 344667788877766666653 222222 35788888877443100 0111
Q ss_pred CCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 236 AIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
....+-++.|-...-|.+||++|.++++|...||-.-.+-+.
T Consensus 73 -------------Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 73 -------------FDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred -------------ecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 122456788888999999999999999999999988888764
No 107
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=90.54 E-value=0.17 Score=35.95 Aligned_cols=36 Identities=36% Similarity=0.624 Sum_probs=28.8
Q ss_pred EEEEecCCc-----cceeecccChhhhhhhhcc-CcEEEEec
Q 020173 52 FRIIVPSRQ-----IGKVIGKEGHRIQKIREET-KATIKIAD 87 (330)
Q Consensus 52 ~~i~vP~~~-----vg~IIGk~G~~Ik~I~~~t-g~~I~i~~ 87 (330)
.++.|-+.. +|..||++|.+|+.|.++. |-+|+|-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 456666766 9999999999999999999 88888754
No 108
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.04 E-value=0.1 Score=55.02 Aligned_cols=71 Identities=20% Similarity=0.153 Sum_probs=55.0
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC-CCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhh
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA-IARHEERVIIISSKDNDNVVSDAENALQQIAALILK 124 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~-~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~ 124 (330)
....++.+|.....++||++|.+|..++.-||+.|.+.+- ..+..||.+.+.|.+ ....-|...|.-.+.+
T Consensus 1339 ~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p-----~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1339 ANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRP-----PSQRVATSPIGLPIID 1410 (2131)
T ss_pred ccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCC-----hhhhhhhccccceeec
Confidence 3456788999999999999999999999999999999873 345678999999987 3344454444444433
No 109
>PRK12705 hypothetical protein; Provisional
Probab=89.99 E-value=0.38 Score=47.56 Aligned_cols=41 Identities=27% Similarity=0.436 Sum_probs=35.3
Q ss_pred CceEEEEEecC-CccceeecccChhhhhhhhccCcEEEEecC
Q 020173 48 QDVLFRIIVPS-RQIGKVIGKEGHRIQKIREETKATIKIADA 88 (330)
Q Consensus 48 ~~~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (330)
...+--+.+|+ +.-|.||||.|.||+.++..||+.|-|++.
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt 237 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT 237 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC
Confidence 34556677788 569999999999999999999999999874
No 110
>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=89.89 E-value=0.58 Score=32.27 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=27.2
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeE
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMI 285 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I 285 (330)
....+.+.....|.+||++|++++.|+..++-.+
T Consensus 25 ~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 25 IEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred EEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 4555666665689999999999999999988554
No 111
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=89.64 E-value=0.74 Score=41.34 Aligned_cols=51 Identities=16% Similarity=0.249 Sum_probs=45.3
Q ss_pred ceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 155 g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 219 (330)
-++||++|++++.|+--|.|.|-+. ...|.+.|....+.++...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVq--------------G~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQ--------------GNTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEee--------------CcEEEeecCcchHHHHHHHHHHHHhc
Confidence 5699999999999999999999884 24799999999999999999998875
No 112
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=89.61 E-value=0.71 Score=41.44 Aligned_cols=51 Identities=20% Similarity=0.283 Sum_probs=44.9
Q ss_pred cceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 264 GGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 264 g~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
-++||.+|++++.|+-.|.|.|-|.. .+|.+.|....+..+.+.+.+-+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC-------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 47999999999999999999999995 3688999999999999988876543
No 113
>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=88.73 E-value=0.43 Score=34.56 Aligned_cols=34 Identities=18% Similarity=0.407 Sum_probs=26.9
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCcEEE
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIK 84 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~ 84 (330)
.+.+.+.....|.+|||+|.++..||--++.-++
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 3556667788999999999999999977664444
No 114
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=88.04 E-value=0.58 Score=33.87 Aligned_cols=36 Identities=25% Similarity=0.350 Sum_probs=28.8
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEE
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV 287 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i 287 (330)
....+.|..+..|.+||++|+++..||--+..-++-
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 345677788889999999999999998877654443
No 115
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=87.43 E-value=1.7 Score=42.38 Aligned_cols=127 Identities=13% Similarity=0.046 Sum_probs=81.7
Q ss_pred eecCCCChhHHHHHHHhCCeE--EEeCCCCCCcccCCCCCCcEEE-EEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCC
Q 020173 156 CLIGMSGQNIEKLRNSSGATI--VILAPNQLPLCASAHESDRVVQ-ISGDVPAVLNALVEIGNQLRENPPRQVISISPAY 232 (330)
Q Consensus 156 ~iIG~~G~~Ik~I~~~sga~I--~i~~~~~~p~~~~~~~~~r~v~-I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~ 232 (330)
+|-|++.-++..|.+...|-+ .+... ...++.+ +.|..-...++...+.+ .
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~----------~gs~~~~~~~g~~~~F~k~~~~~~~----E------------ 446 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSS----------TGSIVETNGIGEKMSFSKKLSIPPT----E------------ 446 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEec----------CCcEEEEeccCcchhhHHHhcCCcc----c------------
Confidence 677877777999999888874 44332 1223333 45665555544433211 1
Q ss_pred CCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCCC--CCceeE-EEEEcC---HH
Q 020173 233 NYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGKG--EQKHRH-IQFGGS---AQ 306 (330)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~--~~~~r~-v~I~Gt---~~ 306 (330)
-.....|.||...|..|||.||..|++.+...++.|++..... .+..+. |.|.-+ .+
T Consensus 447 -----------------Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~dNV~I~~PrKn~~ 509 (657)
T COG5166 447 -----------------FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHDNVLIEAPRKNQD 509 (657)
T ss_pred -----------------CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhcceEEECCccCcc
Confidence 1244679999999999999999999999999999999886432 333333 666654 33
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 020173 307 QVALAKQRVDEYIYSQLIQ 325 (330)
Q Consensus 307 ~v~~A~~~I~~~i~~~~~~ 325 (330)
++-.++.-+.+++.+++.-
T Consensus 510 ni~~~KNd~~~~V~~~c~f 528 (657)
T COG5166 510 NISGKKNDKLDKVKQQCRF 528 (657)
T ss_pred chhcccccHHHHHhhhccc
Confidence 4444555566666655533
No 116
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=87.20 E-value=0.39 Score=34.74 Aligned_cols=34 Identities=35% Similarity=0.461 Sum_probs=28.6
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeE
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMI 285 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I 285 (330)
....+.+....-|.+||++|++|++|....+-.+
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 4567888999999999999999999987765544
No 117
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=87.04 E-value=1.9 Score=38.09 Aligned_cols=46 Identities=22% Similarity=0.480 Sum_probs=38.0
Q ss_pred EEEecCCccceeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCC
Q 020173 53 RIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDN 104 (330)
Q Consensus 53 ~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~ 104 (330)
-+.||...+.++||++|+.++.|.+.|+|.|-+-.. -.|-|.+..+
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~ 194 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENE 194 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCc
Confidence 467899999999999999999999999999999652 3366666553
No 118
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.94 E-value=1.8 Score=38.21 Aligned_cols=38 Identities=26% Similarity=0.297 Sum_probs=34.9
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
-.-+.||+..+.++||++|+.++-|.+.|+|+|.+-.+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N 184 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN 184 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC
Confidence 35688999999999999999999999999999999965
No 119
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.20 E-value=0.64 Score=34.13 Aligned_cols=36 Identities=19% Similarity=0.423 Sum_probs=30.5
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCcEEEEe
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIA 86 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~ 86 (330)
..++.|....-|.|||++|++|++|+++-.-...+.
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 478888999999999999999999998876665553
No 120
>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=85.75 E-value=0.61 Score=33.70 Aligned_cols=33 Identities=36% Similarity=0.595 Sum_probs=27.9
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeE
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATI 176 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I 176 (330)
...+.+...+.+.+||++|++|++|.....-.+
T Consensus 26 ~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l 58 (78)
T PF07650_consen 26 QIIIVIKASQPGIVIGKKGSNIKKIREELRKEL 58 (78)
T ss_dssp EEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHH
T ss_pred eEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHH
Confidence 578889999999999999999999887755443
No 121
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=85.68 E-value=0.4 Score=46.30 Aligned_cols=39 Identities=33% Similarity=0.454 Sum_probs=34.9
Q ss_pred eEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC
Q 020173 50 VLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (330)
Q Consensus 50 ~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (330)
-...+.||.++.+.+|||+|.+|++|++..|-+|.|-..
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 345678899999999999999999999999999999764
No 122
>PRK13764 ATPase; Provisional
Probab=85.24 E-value=0.48 Score=47.95 Aligned_cols=41 Identities=37% Similarity=0.528 Sum_probs=36.2
Q ss_pred CceEEEEEecCCccceeecccChhhhhhhhccCcEEEEecC
Q 020173 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIADA 88 (330)
Q Consensus 48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~~ 88 (330)
.+-..-+.||.+.++.+|||+|.+|++|++..|..|+|...
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~ 519 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPL 519 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEc
Confidence 34455788899999999999999999999999999999764
No 123
>PRK13764 ATPase; Provisional
Probab=84.90 E-value=6.8 Score=39.81 Aligned_cols=43 Identities=21% Similarity=0.358 Sum_probs=38.3
Q ss_pred eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCC
Q 020173 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLP 185 (330)
Q Consensus 143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p 185 (330)
....+.||...++.+|||+|.+|++|+++.|..|.+...+..+
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 3678999999999999999999999999999999998765443
No 124
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=84.59 E-value=2.5 Score=41.09 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=35.9
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCC
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPN 182 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~ 182 (330)
...+.+|..+.+.+||++|.+|++|+++.|.+|.+...+
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 678899999999999999999999999999999997643
No 125
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=83.14 E-value=5.7 Score=32.41 Aligned_cols=92 Identities=14% Similarity=0.313 Sum_probs=62.3
Q ss_pred ccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccccccCCCcceEEE
Q 020173 67 KEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAANTIR 146 (330)
Q Consensus 67 k~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~ 146 (330)
.+|.-|++|-++..-+|.|.... + + +..-.+|.+.|.+++-++..-..-.+ ...+-+
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~dp---s-----~--------l~~~e~A~~~I~~ivP~ea~i~di~F-------d~~tGE 79 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRPDP---S-----V--------LKPPEEAIKIILEIVPEEAGITDIYF-------DDDTGE 79 (145)
T ss_pred cccHHHHHHHHHHhceEEEcCCh---h-----h--------cCCHHHHHHHHHHhCCCccCceeeEe-------cCCCcE
Confidence 45778888888888888886431 0 0 11225788888887643322111111 112457
Q ss_pred EEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (330)
Q Consensus 147 llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~ 181 (330)
+.|-...-|++||++|.++++|..++|-.-.+...
T Consensus 80 V~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 80 VIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred EEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 78888889999999999999999999988887653
No 126
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=82.78 E-value=1.2 Score=37.35 Aligned_cols=38 Identities=21% Similarity=0.352 Sum_probs=32.2
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccCcEEEEec
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKIAD 87 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i~~ 87 (330)
+-.+-++|-... |.-|||+|.+++++++..|-+|.+-.
T Consensus 60 ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 60 DDLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred CCEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 445566777777 99999999999999999998888865
No 127
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=80.56 E-value=2.6 Score=35.37 Aligned_cols=39 Identities=15% Similarity=0.191 Sum_probs=33.2
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK 291 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~ 291 (330)
...-|.|.... |.-||++|++++.+++..|-+|.+-...
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~s 99 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEKT 99 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEcC
Confidence 45567777777 9999999999999999999999998653
No 128
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.38 E-value=1.4 Score=32.58 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=23.6
Q ss_pred EEEEecCCccceeecccChhhhhhhhcc
Q 020173 52 FRIIVPSRQIGKVIGKEGHRIQKIREET 79 (330)
Q Consensus 52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~t 79 (330)
.++.|....-|.+||++|.+|++|++..
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 5666667899999999999999988664
No 129
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.00 E-value=1.2 Score=34.60 Aligned_cols=31 Identities=29% Similarity=0.549 Sum_probs=26.3
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCc
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~ 81 (330)
.++|.|....-|.|||++|++|++|++....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 3678888889999999999999999876543
No 130
>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=78.07 E-value=2.7 Score=30.81 Aligned_cols=37 Identities=14% Similarity=0.219 Sum_probs=29.6
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEEe
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVY 288 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~ 288 (330)
...++.|-...-|.+||++|+.|++|++.......++
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3467788888889999999999999988866555554
No 131
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=74.92 E-value=8.7 Score=37.83 Aligned_cols=96 Identities=17% Similarity=0.311 Sum_probs=67.6
Q ss_pred eeecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccccccCCCcc
Q 020173 63 KVIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAA 142 (330)
Q Consensus 63 ~IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~ 142 (330)
.++-+.|.-|++|-++..-+|.|.... . + +..-.+|.+.|.+++-++..-....+. .
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP---s---v----------l~~~e~A~~~I~eivP~ea~i~~i~Fd-------~ 98 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP---S---V----------LKPPEEARKIILEIVPEEAGITDIYFD-------D 98 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc---h---h----------cCCHHHHHHHHHHhCccccCceeEEec-------C
Confidence 345578899999999999999987531 0 0 123368888888877443322111111 1
Q ss_pred eEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173 143 NTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (330)
Q Consensus 143 ~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~ 181 (330)
.+-.++|-...-|.+||++|++.+.|..++|-.-.+.+.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 245788888999999999999999999999977777653
No 132
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=74.27 E-value=2.2 Score=37.53 Aligned_cols=32 Identities=34% Similarity=0.525 Sum_probs=26.5
Q ss_pred ceEEEEEecCCccceeecccChhhhhhhhccC
Q 020173 49 DVLFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (330)
Q Consensus 49 ~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg 80 (330)
....++.|....-|.|||++|++|++|++...
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 34567888999999999999999999886543
No 133
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=72.41 E-value=7.6 Score=39.81 Aligned_cols=97 Identities=24% Similarity=0.205 Sum_probs=64.4
Q ss_pred eecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCC
Q 020173 156 CLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYS 235 (330)
Q Consensus 156 ~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~ 235 (330)
..+-.+|.-|++|..+---+|.|-.. .. +.-++ .+|.+.|.+++-++-.- .+..
T Consensus 36 ~~~~~~~~~~~~~~~~~~~r~~~~~~------------~~---~~~~~---~~~~~~i~~~~~~~~~~------~~~~-- 89 (630)
T TIGR03675 36 ELFAKDDDLVKELAKKLRKRIVIRPD------------PS---VLLPP---EEAIEKIKEIVPEEAGI------TDIY-- 89 (630)
T ss_pred HHhccchHHHHHHHHHhhceEEEecC------------hh---hcCCH---HHHHHHHHHhCCCcCCc------eeEE--
Confidence 34556678889998887777776321 00 11112 34777777777443110 0011
Q ss_pred CCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCCC
Q 020173 236 AIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGGK 291 (330)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~ 291 (330)
....+-++.|-...-|.+|||+|.++++|..+||-.-.+-+..
T Consensus 90 -------------f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 90 -------------FDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred -------------ecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 1224567888899999999999999999999999888887643
No 134
>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=70.41 E-value=4.3 Score=31.49 Aligned_cols=30 Identities=30% Similarity=0.485 Sum_probs=24.4
Q ss_pred EEEEEccccccceecCCCchHHHHHHHhCC
Q 020173 254 FEMLISESLVGGLIGRCGSNISRIRNESGA 283 (330)
Q Consensus 254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga 283 (330)
+.+.|-...-|.|||++|+.|++|+.....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~ 92 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQK 92 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHH
Confidence 567777777899999999999999776443
No 135
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=66.45 E-value=6.9 Score=28.80 Aligned_cols=28 Identities=29% Similarity=0.366 Sum_probs=22.3
Q ss_pred EEEEEccccccceecCCCchHHHHHHHh
Q 020173 254 FEMLISESLVGGLIGRCGSNISRIRNES 281 (330)
Q Consensus 254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~t 281 (330)
..+.|-...-|.+||++|+.|++|+..-
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l 67 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEIL 67 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHH
Confidence 4555666777999999999999987653
No 136
>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=61.22 E-value=25 Score=36.07 Aligned_cols=95 Identities=15% Similarity=0.280 Sum_probs=64.7
Q ss_pred eecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcCCCCccccccccCCCcce
Q 020173 64 VIGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKDDDSNSEASKVAAGHVAAN 143 (330)
Q Consensus 64 IIGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~~~~~~~~~~~~~~~~~~ 143 (330)
.+=.+|..|++|-++..-+|.|.... + +. ..-.+|.+.|.+++-++..-..-.+ ...
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~---~-----~~--------~~~~~~~~~i~~~~~~~~~~~~~~f-------~~~ 93 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDP---S-----VL--------LPPEEAIEKIKEIVPEEAGITDIYF-------DDV 93 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecCh---h-----hc--------CCHHHHHHHHHHhCCCcCCceeEEe-------cCC
Confidence 34466788899998888888886431 0 01 1225788888887643322111011 112
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCC
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAP 181 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~ 181 (330)
+-+++|-...-|.+||++|.++++|..++|-.-.+.+.
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 45788888999999999999999999999988887653
No 137
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=59.14 E-value=26 Score=32.93 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=44.1
Q ss_pred cccccceecCCCchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHH
Q 020173 260 ESLVGGLIGRCGSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVD 316 (330)
Q Consensus 260 ~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~ 316 (330)
++.+-.+.|..|.+++.|...+|++|.... +.++|.|+...++.|...+.
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG-------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARG-------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCC-------ceEEEEechHHHHHHHHHHh
Confidence 567789999999999999999999998875 46899999779999988887
No 138
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=56.42 E-value=13 Score=33.55 Aligned_cols=28 Identities=21% Similarity=0.209 Sum_probs=21.9
Q ss_pred eEEEEEEccccc-cceecCCCchHHHHHH
Q 020173 252 VTFEMLISESLV-GGLIGRCGSNISRIRN 279 (330)
Q Consensus 252 ~~~~v~IP~~~v-g~IIGk~G~~Ik~i~~ 279 (330)
....+.|..+-. +.|||++|++||+|..
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~ 249 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGI 249 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHH
Confidence 556677776654 9999999999998744
No 139
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=54.86 E-value=13 Score=32.91 Aligned_cols=28 Identities=43% Similarity=0.684 Sum_probs=24.0
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHH
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNS 171 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~ 171 (330)
.+++.|....-|.+||++|++|++|++.
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 5788888888999999999999887654
No 140
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=52.45 E-value=11 Score=32.84 Aligned_cols=31 Identities=29% Similarity=0.482 Sum_probs=25.3
Q ss_pred EEEEecCCccceeecccChhhhhhhhccCcE
Q 020173 52 FRIIVPSRQIGKVIGKEGHRIQKIREETKAT 82 (330)
Q Consensus 52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~ 82 (330)
.++.|....-|.+||++|++|++|++.-.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~ 72 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKK 72 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHH
Confidence 5666666889999999999999998776543
No 141
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=51.42 E-value=12 Score=32.29 Aligned_cols=31 Identities=29% Similarity=0.529 Sum_probs=26.3
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCc
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKA 81 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~ 81 (330)
..++.|....-|.+||++|..|++|++.-.-
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 4678888889999999999999999876543
No 142
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=51.37 E-value=19 Score=35.58 Aligned_cols=97 Identities=25% Similarity=0.223 Sum_probs=65.7
Q ss_pred ceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCC
Q 020173 155 GCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNY 234 (330)
Q Consensus 155 g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~ 234 (330)
..++-+.|.-|++|..+---+|.+-+ | |. + ...-..|.+.|.+++-++-.- .++.
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~-d--Ps----------v-----l~~~e~A~~~I~eivP~ea~i------~~i~- 95 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRP-D--PS----------V-----LKPPEEARKIILEIVPEEAGI------TDIY- 95 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEecc-C--ch----------h-----cCCHHHHHHHHHHhCccccCc------eeEE-
Confidence 34666788899999999888888743 2 10 0 011235777787777443110 0000
Q ss_pred CCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHHHHhCCeEEEeCC
Q 020173 235 SAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKVYGG 290 (330)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i~~~ 290 (330)
....+-++.|-...-|.+|||+|++.++|..+||-.-+|-+.
T Consensus 96 --------------Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 96 --------------FDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred --------------ecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 122456788888999999999999999999999987777754
No 143
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=51.28 E-value=40 Score=29.28 Aligned_cols=36 Identities=17% Similarity=0.268 Sum_probs=30.5
Q ss_pred eEEEEEEccccccceecCCCchHHHHHHHhCCeEEE
Q 020173 252 VTFEMLISESLVGGLIGRCGSNISRIRNESGAMIKV 287 (330)
Q Consensus 252 ~~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga~I~i 287 (330)
.++.+.|-.+..+.+||+.|+++..||-.+.+-++-
T Consensus 91 ~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 91 RRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 566778888889999999999999999888765555
No 144
>CHL00048 rps3 ribosomal protein S3
Probab=51.27 E-value=12 Score=32.85 Aligned_cols=30 Identities=17% Similarity=0.339 Sum_probs=25.6
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccC
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg 80 (330)
..++.|-...-|.|||++|.+|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 467777888899999999999999997764
No 145
>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=50.75 E-value=14 Score=33.38 Aligned_cols=29 Identities=31% Similarity=0.308 Sum_probs=23.1
Q ss_pred eEEEEEecC-CccceeecccChhhhhhhhc
Q 020173 50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREE 78 (330)
Q Consensus 50 ~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~ 78 (330)
+...|+|.. ++.+-|||++|+.||+|..+
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 566777776 56899999999999988654
No 146
>COG1159 Era GTPase [General function prediction only]
Probab=49.39 E-value=20 Score=32.93 Aligned_cols=37 Identities=19% Similarity=0.344 Sum_probs=26.3
Q ss_pred eEEEEEEccccc-cceecCCCchHHHH--------HHHhCCeEEEe
Q 020173 252 VTFEMLISESLV-GGLIGRCGSNISRI--------RNESGAMIKVY 288 (330)
Q Consensus 252 ~~~~v~IP~~~v-g~IIGk~G~~Ik~i--------~~~tga~I~i~ 288 (330)
....+.|+.+-. |.||||+|++||+| ++..+++|.+.
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~ 274 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLE 274 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhCCceEEE
Confidence 445567776644 99999999999986 44456665554
No 147
>COG1159 Era GTPase [General function prediction only]
Probab=49.19 E-value=16 Score=33.60 Aligned_cols=30 Identities=37% Similarity=0.485 Sum_probs=23.5
Q ss_pred ceEEEEEecC-CccceeecccChhhhhhhhc
Q 020173 49 DVLFRIIVPS-RQIGKVIGKEGHRIQKIREE 78 (330)
Q Consensus 49 ~~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~ 78 (330)
.+...|+|+- ++-|-||||+|+.||+|-..
T Consensus 228 ~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 228 KIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 3555677776 56899999999999987643
No 148
>PRK15494 era GTPase Era; Provisional
Probab=48.95 E-value=20 Score=33.72 Aligned_cols=37 Identities=19% Similarity=0.345 Sum_probs=27.1
Q ss_pred eEEEEEEccccc-cceecCCCchHHHH--------HHHhCCeEEEe
Q 020173 252 VTFEMLISESLV-GGLIGRCGSNISRI--------RNESGAMIKVY 288 (330)
Q Consensus 252 ~~~~v~IP~~~v-g~IIGk~G~~Ik~i--------~~~tga~I~i~ 288 (330)
....+.|..+-+ +.|||++|++||+| ++..|++|.+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 445677777655 99999999999986 45566666554
No 149
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=48.22 E-value=14 Score=32.60 Aligned_cols=33 Identities=21% Similarity=0.424 Sum_probs=27.1
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccCcEE
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETKATI 83 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I 83 (330)
..++.|....-|.|||++|..|++|++...-.+
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 367778888899999999999999987765443
No 150
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=47.19 E-value=13 Score=32.21 Aligned_cols=38 Identities=13% Similarity=0.306 Sum_probs=30.5
Q ss_pred CceEEEEEecCCccceeecccChhhhhhhhccCcEEEE
Q 020173 48 QDVLFRIIVPSRQIGKVIGKEGHRIQKIREETKATIKI 85 (330)
Q Consensus 48 ~~~~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg~~I~i 85 (330)
..-.+.+.+-.+..+.+||+.|.++..||--++..++-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34455666777789999999999999999888866655
No 151
>PRK00089 era GTPase Era; Reviewed
Probab=46.70 E-value=23 Score=32.28 Aligned_cols=37 Identities=16% Similarity=0.317 Sum_probs=26.2
Q ss_pred eEEEEEEccccc-cceecCCCchHHHH--------HHHhCCeEEEe
Q 020173 252 VTFEMLISESLV-GGLIGRCGSNISRI--------RNESGAMIKVY 288 (330)
Q Consensus 252 ~~~~v~IP~~~v-g~IIGk~G~~Ik~i--------~~~tga~I~i~ 288 (330)
....+.|..+-. +.|||++|++||+| ++..+++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 445566665544 99999999999986 45567666554
No 152
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=46.63 E-value=73 Score=23.39 Aligned_cols=52 Identities=13% Similarity=0.157 Sum_probs=41.6
Q ss_pred CCchHHHHHHHhCCeEEEeCCCC---CCceeEEEEEcCHHHHHHHHHHHHHHHHH
Q 020173 270 CGSNISRIRNESGAMIKVYGGKG---EQKHRHIQFGGSAQQVALAKQRVDEYIYS 321 (330)
Q Consensus 270 ~G~~Ik~i~~~tga~I~i~~~~~---~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~ 321 (330)
|=....++-+..++++.....+. ...+.++++.|+..++..|.+.++.+|..
T Consensus 32 G~~~~~~i~~~l~~~v~~~~~dG~~v~~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 32 GLEEAEEIFEKLGLEVEWLVKDGDRVEPGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp SHHHHHHHHHHCTEEEEESS-TT-EEETTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhhccEEEEEEeCCCCCccCCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 44677888888899888875543 34689999999999999999999888753
No 153
>PRK15494 era GTPase Era; Provisional
Probab=45.78 E-value=18 Score=34.01 Aligned_cols=29 Identities=24% Similarity=0.410 Sum_probs=23.0
Q ss_pred eEEEEEecC-CccceeecccChhhhhhhhc
Q 020173 50 VLFRIIVPS-RQIGKVIGKEGHRIQKIREE 78 (330)
Q Consensus 50 ~~~~i~vP~-~~vg~IIGk~G~~Ik~I~~~ 78 (330)
+...|+|.. ++-+-|||++|+.||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 556777776 56889999999999988643
No 154
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=44.21 E-value=78 Score=26.47 Aligned_cols=57 Identities=21% Similarity=0.286 Sum_probs=42.4
Q ss_pred ceEEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHh
Q 020173 142 ANTIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (330)
Q Consensus 142 ~~~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~ 218 (330)
..+.|+-++...+- +++..|.+-+|+-+.+. ++..|.|-|..+.|..|++.+.....
T Consensus 112 ~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Efe-------------e~~~V~I~Gdke~Ik~aLKe~s~~wk 168 (169)
T PF09869_consen 112 FETIRVKLKKPIQE-------ERLQEISEWHGVIFEFE-------------EDDKVVIEGDKERIKKALKEFSSFWK 168 (169)
T ss_pred ceeEEEecCccchH-------HHHHHHHHHhceeEEec-------------CCcEEEEeccHHHHHHHHHHHHHHhc
Confidence 34556655554433 46889999999877762 35579999999999999998876643
No 155
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=44.02 E-value=62 Score=30.45 Aligned_cols=51 Identities=25% Similarity=0.252 Sum_probs=42.0
Q ss_pred eccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHH
Q 020173 150 AGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIG 214 (330)
Q Consensus 150 p~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~ 214 (330)
+...+-.+.|..+.+++.|+..+|++|... .+.++|.|....+..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r--------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR--------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC--------------CceEEEEechHHHHHHHHHHh
Confidence 356678899999999999999999888742 357999999778887877776
No 156
>PRK00089 era GTPase Era; Reviewed
Probab=40.38 E-value=33 Score=31.22 Aligned_cols=37 Identities=22% Similarity=0.396 Sum_probs=25.6
Q ss_pred eEEEEEee-ccccceecCCCChhHHHHH--------HHhCCeEEEe
Q 020173 143 NTIRLLIA-GSQAGCLIGMSGQNIEKLR--------NSSGATIVIL 179 (330)
Q Consensus 143 ~~~~llip-~~~~g~iIG~~G~~Ik~I~--------~~sga~I~i~ 179 (330)
+...++|. .++-+.|||++|+.||+|. +-++++|.+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 34455555 3567889999999998865 4467766653
No 157
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=39.67 E-value=22 Score=33.02 Aligned_cols=32 Identities=25% Similarity=0.461 Sum_probs=26.0
Q ss_pred ceEEEEEecCC-ccceeecccChhhhhhhhccC
Q 020173 49 DVLFRIIVPSR-QIGKVIGKEGHRIQKIREETK 80 (330)
Q Consensus 49 ~~~~~i~vP~~-~vg~IIGk~G~~Ik~I~~~tg 80 (330)
.+..++.||.. ....|||+||..|++|-++-+
T Consensus 327 ~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 327 FIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 36778899985 577899999999999976654
No 158
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=38.97 E-value=61 Score=30.21 Aligned_cols=34 Identities=24% Similarity=0.354 Sum_probs=26.1
Q ss_pred CcceEEEEEeec-cccceecCCCChhHHHHHHHhC
Q 020173 140 VAANTIRLLIAG-SQAGCLIGMSGQNIEKLRNSSG 173 (330)
Q Consensus 140 ~~~~~~~llip~-~~~g~iIG~~G~~Ik~I~~~sg 173 (330)
.-.+..++++|. ++...|||++|..|++|-.+.+
T Consensus 325 ~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 325 VLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred EEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 344567788885 5677899999999999887654
No 159
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=36.85 E-value=54 Score=28.88 Aligned_cols=31 Identities=16% Similarity=0.260 Sum_probs=24.6
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHhCC
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNESGA 283 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga 283 (330)
..++.|-...-|.|||++|..|++|++...-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k 75 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQK 75 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHH
Confidence 3567777777899999999999998766543
No 160
>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=36.11 E-value=38 Score=29.23 Aligned_cols=29 Identities=24% Similarity=0.352 Sum_probs=23.8
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHh
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNES 281 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t 281 (330)
..++.|-...-|.+||++|+.|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 36677777778999999999999986654
No 161
>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=35.64 E-value=92 Score=24.19 Aligned_cols=52 Identities=15% Similarity=0.348 Sum_probs=34.8
Q ss_pred ecccChhhhhhhhccCcEEEEecCCCCCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhc
Q 020173 65 IGKEGHRIQKIREETKATIKIADAIARHEERVIIISSKDNDNVVSDAENALQQIAALILKD 125 (330)
Q Consensus 65 IGk~G~~Ik~I~~~tg~~I~i~~~~~~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~ 125 (330)
=|+||.++++.. |.|.|...+. . ++|.....-....|-..|+..+.+.|...
T Consensus 22 sGpGGQ~VNk~~--s~V~l~h~pt-----g--i~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~ 73 (113)
T PF00472_consen 22 SGPGGQNVNKTN--SKVRLRHIPT-----G--IVVKCQESRSQHQNREDALEKLREKLDEA 73 (113)
T ss_dssp SSSSSCHHHSSS--EEEEEEETTT-----T--EEEEEESSSSHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCcccccC--CEEEEEEecc-----c--EEEEEcccCCHHHHHHHHHHHHHHHHHHH
Confidence 389999998753 4466666532 1 55555555455678888888888877543
No 162
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=34.13 E-value=30 Score=30.29 Aligned_cols=29 Identities=34% Similarity=0.692 Sum_probs=24.8
Q ss_pred EEEEecCCccceeecccChhhhhhhhccC
Q 020173 52 FRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (330)
Q Consensus 52 ~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg 80 (330)
++|.|....-|.|||++|.+|++|++.-.
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 66788888889999999999999986654
No 163
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=33.68 E-value=1.3e+02 Score=22.06 Aligned_cols=67 Identities=22% Similarity=0.283 Sum_probs=45.0
Q ss_pred EEeeccccceecCCCChhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173 147 LLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 147 llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 219 (330)
..+=.+.-+.+-|. .-+.++-+..++.+....+|.-.-. ..+.++++.|+..++..|.+.++..+..
T Consensus 20 a~i~are~gV~aG~--~~~~~i~~~l~~~v~~~~~dG~~v~----~g~~i~~i~G~a~~ll~~ER~~LN~l~~ 86 (88)
T PF02749_consen 20 ATIIAREDGVLAGL--EEAEEIFEKLGLEVEWLVKDGDRVE----PGDVILEIEGPARALLTAERTALNFLQR 86 (88)
T ss_dssp EEEEESSSEEE-SH--HHHHHHHHHCTEEEEESS-TT-EEE----TTCEEEEEEEEHHHHHHHHHHHHHHHHH
T ss_pred EEEEeCCCEEEECH--HHHHHHHhhccEEEEEEeCCCCCcc----CCcEEEEEEeCHHHHHHHHHHHHHHHHH
Confidence 33333333555433 3567777888998988766543221 3568999999999999999999988753
No 164
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=33.61 E-value=43 Score=29.19 Aligned_cols=30 Identities=27% Similarity=0.314 Sum_probs=23.3
Q ss_pred EEEEEccccccceecCCCchHHHHHHHhCC
Q 020173 254 FEMLISESLVGGLIGRCGSNISRIRNESGA 283 (330)
Q Consensus 254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~tga 283 (330)
..+.|-...-|.+||++|++|++++..-.-
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk 71 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEK 71 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHH
Confidence 455555577899999999999998776543
No 165
>CHL00048 rps3 ribosomal protein S3
Probab=33.21 E-value=43 Score=29.32 Aligned_cols=29 Identities=21% Similarity=0.274 Sum_probs=23.6
Q ss_pred EEEEEEccccccceecCCCchHHHHHHHh
Q 020173 253 TFEMLISESLVGGLIGRCGSNISRIRNES 281 (330)
Q Consensus 253 ~~~v~IP~~~vg~IIGk~G~~Ik~i~~~t 281 (330)
..++.|-...-|.|||++|+.|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 35666667777999999999999987765
No 166
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=32.26 E-value=2.6e+02 Score=24.55 Aligned_cols=121 Identities=15% Similarity=0.138 Sum_probs=67.2
Q ss_pred CcEEEEEc-CHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCCCCCCCCC---CCCCCCcceEEEEEEcccc-ccceec
Q 020173 194 DRVVQISG-DVPAVLNALVEIGNQLRENPPRQVISISPAYNYSAIRPAQPF---VEPTSADYVTFEMLISESL-VGGLIG 268 (330)
Q Consensus 194 ~r~v~I~G-~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~v~IP~~~-vg~IIG 268 (330)
+-++.|.| +...|..|++...+.+++...-- ..+.. -+-.+ ..+.........+-+|... .|.|||
T Consensus 82 ~viiIi~G~dvsdVrsAveaa~~~i~~~~~f~--~~n~~-------g~~~~~a~~~aRag~~l~k~~g~~~G~a~~~li~ 152 (217)
T PRK15405 82 EVIGILAGPNPAEVRAGLDAMVAFIENGAAFQ--SANDD-------DSTAFFAHVVSRTGSYLSKTAGIAEGEPLAYLIA 152 (217)
T ss_pred cEEEEEeCCCHHHHHHHHHHHHHHHHhhhceE--eeCCC-------CCEEEEEEEcccHHHHHHHHcCCCCCceeEEEec
Confidence 33678999 99999999999999998752110 00000 00000 0000111122234444443 377777
Q ss_pred CCCchHHHH---HHHhCCeEE-EeCCCCCCceeEEEEEcCHHHHHHHHHHHHHHHHHHH
Q 020173 269 RCGSNISRI---RNESGAMIK-VYGGKGEQKHRHIQFGGSAQQVALAKQRVDEYIYSQL 323 (330)
Q Consensus 269 k~G~~Ik~i---~~~tga~I~-i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~~i~~~~ 323 (330)
.=+.-+--+ .+...+++. +..+..++.---..|+|+...|..|.....+.++...
T Consensus 153 ~P~~~~~~~D~AlKaA~V~~~~~~~P~~~t~f~~~~ltG~~~A~r~A~~a~~e~v~~~a 211 (217)
T PRK15405 153 PPLEAMYGIDAALKAADVQLVTFVGPPSETNFGGALLTGSQSACKAACNAFTDAVLEVA 211 (217)
T ss_pred CcHHHHHHHHHHHhhcCceEEEEeCCCCCceecCeeEEeCHHHHHHHHHHHHHHHHHHH
Confidence 765554443 233445553 3333333332338899999999999888887776543
No 167
>PRK09256 hypothetical protein; Provisional
Probab=31.40 E-value=76 Score=25.73 Aligned_cols=60 Identities=23% Similarity=0.392 Sum_probs=37.0
Q ss_pred ecccChhhhhhhhccCcEEEEecC---CC--------------CCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173 65 IGKEGHRIQKIREETKATIKIADA---IA--------------RHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (330)
Q Consensus 65 IGk~G~~Ik~I~~~tg~~I~i~~~---~~--------------~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~ 126 (330)
=|+||.++++.. |.|.|.++-. .| -+.+..+.|...+.=.+..|...|+.++...|....
T Consensus 23 SGPGGQ~VNKt~--SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~~Nr~~al~kL~~~i~~~~ 99 (138)
T PRK09256 23 SGPGGQNVNKVS--TAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQERNREDALERLVALIREAL 99 (138)
T ss_pred CCCCcccccccc--eeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHh
Confidence 488888888754 4444443211 00 012334667666655566788999999999886543
No 168
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.61 E-value=1.9e+02 Score=23.65 Aligned_cols=44 Identities=30% Similarity=0.425 Sum_probs=35.6
Q ss_pred hhHHHHHHHhCCeEEEeCCCCCCcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhh
Q 020173 163 QNIEKLRNSSGATIVILAPNQLPLCASAHESDRVVQISGDVPAVLNALVEIGNQLRE 219 (330)
Q Consensus 163 ~~Ik~I~~~sga~I~i~~~~~~p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~ 219 (330)
++++.|.+-.|+-+.+. .-..|.|-|+.+.|.+|++.+.....+
T Consensus 126 eRlqDi~E~hgvIiE~~-------------E~D~V~i~Gd~drVk~aLke~~~~wke 169 (170)
T COG4010 126 ERLQDIAETHGVIIEFE-------------EYDLVAIYGDSDRVKKALKEIGSFWKE 169 (170)
T ss_pred HHHHHHHHhhheeEEee-------------eccEEEEeccHHHHHHHHHHHHHHHhc
Confidence 46778888899877774 345899999999999999999877543
No 169
>PRK03818 putative transporter; Validated
Probab=27.84 E-value=6.5e+02 Score=25.46 Aligned_cols=138 Identities=15% Similarity=0.305 Sum_probs=74.7
Q ss_pred EEEEEeeccccceecCCCChhHHHHHHHhCCeEEEeC--CC-CC--CcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHh
Q 020173 144 TIRLLIAGSQAGCLIGMSGQNIEKLRNSSGATIVILA--PN-QL--PLCASAHESDRVVQISGDVPAVLNALVEIGNQLR 218 (330)
Q Consensus 144 ~~~llip~~~~g~iIG~~G~~Ik~I~~~sga~I~i~~--~~-~~--p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~ 218 (330)
..++.|+++. ++ |.+++++.......+.+.. ++ .. |.....-....++.+.|+.+++.++...+-..+.
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~~~ 279 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEEVD 279 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCccC
Confidence 4566666333 33 6789999888776555532 11 11 1000001245689999999998766554432211
Q ss_pred hCCCCCCcccCCCCCCCCCCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHH--HHHhCCeEEEeCCCC----
Q 020173 219 ENPPRQVISISPAYNYSAIRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRI--RNESGAMIKVYGGKG---- 292 (330)
Q Consensus 219 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i--~~~tga~I~i~~~~~---- 292 (330)
.. .+ ..........+.+|++ .++|+ +++++ ++.+|+.|.=-...+
T Consensus 280 ~~-----------~~------------~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~ 330 (552)
T PRK03818 280 TS-----------LS------------TRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELV 330 (552)
T ss_pred cc-----------cc------------ccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecC
Confidence 00 00 0011234555555654 66664 78887 466776544332111
Q ss_pred ---C---CceeEEEEEcCHHHHHHHHHHHH
Q 020173 293 ---E---QKHRHIQFGGSAQQVALAKQRVD 316 (330)
Q Consensus 293 ---~---~~~r~v~I~Gt~~~v~~A~~~I~ 316 (330)
+ ..-..+.+.|++++++.+.+.+.
T Consensus 331 ~~~d~~Lq~GD~LlVvG~~~~i~~l~~~Lg 360 (552)
T PRK03818 331 ASPDLSLQFGDILNLVGRPEAIDAVANVLG 360 (552)
T ss_pred CCCCCEEecCCEEEEEECHHHHHHHHHHhC
Confidence 0 01246888999999999877544
No 170
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=27.22 E-value=1.7e+02 Score=20.79 Aligned_cols=43 Identities=14% Similarity=0.107 Sum_probs=31.0
Q ss_pred CchHHHHHHHhCCeEEEeCCCCCCceeEEEEEcCHHHHHHHHHHHHH
Q 020173 271 GSNISRIRNESGAMIKVYGGKGEQKHRHIQFGGSAQQVALAKQRVDE 317 (330)
Q Consensus 271 G~~Ik~i~~~tga~I~i~~~~~~~~~r~v~I~Gt~~~v~~A~~~I~~ 317 (330)
-..|.+|.+.++++|.=-. .+.-+++++|+++.++....++..
T Consensus 16 r~ei~~l~~~f~a~ivd~~----~~~~iie~tG~~~kid~fi~~l~~ 58 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS----PDSIIIELTGTPEKIDAFIKLLKP 58 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE----TTEEEEEEEE-HHHHHHHHHHSTG
T ss_pred HHHHHHHHHHhCCEEEEEC----CCEEEEEEcCCHHHHHHHHHHhhh
Confidence 3567788888998776553 256889999999999988776643
No 171
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=24.44 E-value=51 Score=29.28 Aligned_cols=30 Identities=37% Similarity=0.635 Sum_probs=24.3
Q ss_pred EEEEEecCCccceeecccChhhhhhhhccC
Q 020173 51 LFRIIVPSRQIGKVIGKEGHRIQKIREETK 80 (330)
Q Consensus 51 ~~~i~vP~~~vg~IIGk~G~~Ik~I~~~tg 80 (330)
.++|.|-...-+.|||++|.+|++|++...
T Consensus 63 ~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~ 92 (232)
T PRK00310 63 RVRVTIHTARPGIVIGKKGAEIEKLRKELE 92 (232)
T ss_pred eEEEEEEECCCccccCCCcHHHHHHHHHHH
Confidence 356666777889999999999999887654
No 172
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=22.69 E-value=85 Score=27.44 Aligned_cols=28 Identities=29% Similarity=0.506 Sum_probs=23.0
Q ss_pred EEEEEccccccceecCCCchHHHHHHHh
Q 020173 254 FEMLISESLVGGLIGRCGSNISRIRNES 281 (330)
Q Consensus 254 ~~v~IP~~~vg~IIGk~G~~Ik~i~~~t 281 (330)
+++.|-...-|.|||++|+.|++|++..
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l 91 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDL 91 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHH
Confidence 5677777777999999999999987554
No 173
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=21.08 E-value=92 Score=25.97 Aligned_cols=63 Identities=14% Similarity=0.331 Sum_probs=39.3
Q ss_pred eecccChhhhhhhhccCcEEEEecCC--C--------------CCcceEEEEecCCCCcchhHHHHHHHHHHHHHhhcC
Q 020173 64 VIGKEGHRIQKIREETKATIKIADAI--A--------------RHEERVIIISSKDNDNVVSDAENALQQIAALILKDD 126 (330)
Q Consensus 64 IIGk~G~~Ik~I~~~tg~~I~i~~~~--~--------------~~~ervi~I~G~~~~~~~~~~~~A~~~i~~~i~~~~ 126 (330)
--|+||.+++++-...-++..+.... + .+...-+.|.....-..-.++.+|++.+.++|....
T Consensus 49 SSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~~I~~~~ 127 (172)
T KOG3429|consen 49 SSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAAE 127 (172)
T ss_pred cCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHHHHHHHh
Confidence 35999999999876655555544210 0 000111777776543444678899999988886543
No 174
>TIGR03802 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625).
Probab=20.66 E-value=8.9e+02 Score=24.52 Aligned_cols=125 Identities=20% Similarity=0.285 Sum_probs=65.9
Q ss_pred ChhHHHHHHHhCCeEEEe--CCCC-C--CcccCCCCCCcEEEEEcCHHHHHHHHHHHHHHHhhCCCCCCcccCCCCCCCC
Q 020173 162 GQNIEKLRNSSGATIVIL--APNQ-L--PLCASAHESDRVVQISGDVPAVLNALVEIGNQLRENPPRQVISISPAYNYSA 236 (330)
Q Consensus 162 G~~Ik~I~~~sga~I~i~--~~~~-~--p~~~~~~~~~r~v~I~G~~~~v~~A~~~I~~~i~~~~~~~~~~~~~~~~~~~ 236 (330)
|.++.++.......+.+. .++. . |.....-.....+.+.|+.+++.++...+-..+.+.. .
T Consensus 232 GkTl~el~~~~~~~v~I~~I~R~g~~~~p~~dtvL~~GD~L~V~G~~e~L~~l~~~~G~~~~~~~---------~----- 297 (562)
T TIGR03802 232 GKTVGDLENLFAGRVTIERIRRDGKLLTVSPDLVLNAGDVVLVVGRRDAVVQFGAEIGEEVQEVE---------G----- 297 (562)
T ss_pred CCcHHHHHhhhCCCeEEEEEEECCEEEcCCCCCeeCCCCEEEEEECHHHHHHHHHhcCCccCCcc---------c-----
Confidence 457888877664433332 1111 1 1100001234579999999998776654332211100 0
Q ss_pred CCCCCCCCCCCCCcceEEEEEEccccccceecCCCchHHHHH-H-----HhCCeEEEeCCCC-------C---CceeEEE
Q 020173 237 IRPAQPFVEPTSADYVTFEMLISESLVGGLIGRCGSNISRIR-N-----ESGAMIKVYGGKG-------E---QKHRHIQ 300 (330)
Q Consensus 237 ~~~~~~~~~~~~~~~~~~~v~IP~~~vg~IIGk~G~~Ik~i~-~-----~tga~I~i~~~~~-------~---~~~r~v~ 300 (330)
. ........+.+|++ .++| +++++++ + .+|+.|.--...+ + ..-..+.
T Consensus 298 -------~---~~~~~~e~VV~~~S---~liG---kTL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~Ll 361 (562)
T TIGR03802 298 -------L---DVPMETKDVVLTNK---EYNG---KTVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVT 361 (562)
T ss_pred -------c---CCceEEEEEEECCc---ccCC---ccHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEE
Confidence 0 00112445555554 5666 4788886 2 5676554432211 0 0124688
Q ss_pred EEcCHHHHHHHHHHHH
Q 020173 301 FGGSAQQVALAKQRVD 316 (330)
Q Consensus 301 I~Gt~~~v~~A~~~I~ 316 (330)
+.|++++++++.+.+.
T Consensus 362 V~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 362 LVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEeCHHHHHHHHHHcC
Confidence 8999999999877654
Done!