Query 009012
Match_columns 546
No_of_seqs 346 out of 2132
Neff 8.2
Searched_HMMs 46136
Date Thu Mar 28 19:20:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009012.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009012hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2190 PolyC-binding proteins 100.0 4.4E-47 9.6E-52 398.8 34.5 402 5-448 6-413 (485)
2 KOG1676 K-homology type RNA bi 100.0 7.4E-44 1.6E-48 367.3 30.9 334 41-445 52-390 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 4.2E-42 9.1E-47 337.8 22.7 365 37-446 193-566 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 1.1E-33 2.4E-38 263.7 20.6 353 10-444 19-384 (390)
5 KOG1676 K-homology type RNA bi 100.0 5.8E-29 1.3E-33 257.3 22.5 242 39-349 135-385 (600)
6 KOG2193 IGF-II mRNA-binding pr 100.0 4.8E-29 1E-33 245.9 10.0 243 138-447 197-484 (584)
7 KOG2191 RNA-binding protein NO 99.9 3.3E-26 7.1E-31 220.0 20.3 236 41-322 37-282 (402)
8 KOG2192 PolyC-binding hnRNP-K 99.9 1.2E-22 2.6E-27 190.0 16.9 173 282-479 46-218 (390)
9 KOG2191 RNA-binding protein NO 99.9 8.3E-22 1.8E-26 189.8 17.5 251 137-444 36-315 (402)
10 KOG2190 PolyC-binding proteins 99.9 4.3E-21 9.4E-26 202.5 19.8 173 284-464 43-225 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.6 3.6E-14 7.8E-19 131.6 12.1 137 47-215 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.5 4E-14 8.7E-19 131.3 10.1 138 288-444 2-151 (172)
13 PRK13763 putative RNA-processi 99.5 1.5E-13 3.3E-18 128.3 13.4 141 43-215 3-158 (180)
14 PRK13763 putative RNA-processi 99.5 1.7E-13 3.6E-18 128.0 12.0 142 284-444 3-157 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 1.6E-12 3.5E-17 100.7 7.6 64 371-438 1-64 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 3.9E-12 8.5E-17 98.5 7.0 64 141-208 1-64 (65)
17 KOG2279 Kinase anchor protein 99.2 6.4E-11 1.4E-15 122.4 13.2 271 39-339 64-354 (608)
18 cd02394 vigilin_like_KH K homo 99.2 1.6E-11 3.4E-16 94.3 5.8 61 372-439 2-62 (62)
19 KOG2279 Kinase anchor protein 99.2 3.5E-11 7.7E-16 124.3 9.2 232 136-442 64-366 (608)
20 cd02393 PNPase_KH Polynucleoti 99.2 7.3E-11 1.6E-15 89.9 8.0 58 370-438 2-60 (61)
21 KOG2208 Vigilin [Lipid transpo 99.2 4.7E-11 1E-15 133.7 9.2 304 43-445 201-563 (753)
22 PF00013 KH_1: KH domain syndr 99.2 1.8E-11 4E-16 93.2 3.7 60 371-438 1-60 (60)
23 cd00105 KH-I K homology RNA-bi 99.1 2.2E-10 4.9E-15 88.3 8.2 62 372-438 2-63 (64)
24 cd02394 vigilin_like_KH K homo 99.1 1.5E-10 3.3E-15 88.8 5.5 60 142-208 2-61 (62)
25 PF00013 KH_1: KH domain syndr 99.1 7.3E-11 1.6E-15 89.9 3.7 60 141-208 1-60 (60)
26 cd02393 PNPase_KH Polynucleoti 99.1 4.1E-10 9E-15 85.8 7.8 58 140-208 2-60 (61)
27 cd00105 KH-I K homology RNA-bi 99.0 1.2E-09 2.5E-14 84.2 7.6 62 142-208 2-63 (64)
28 PF13014 KH_3: KH domain 98.9 1.8E-09 3.9E-14 76.2 5.7 42 53-94 1-43 (43)
29 KOG2208 Vigilin [Lipid transpo 98.9 4.9E-09 1.1E-13 117.7 8.9 288 43-445 347-636 (753)
30 PF13014 KH_3: KH domain 98.9 4.5E-09 9.7E-14 74.2 5.5 43 380-426 1-43 (43)
31 smart00322 KH K homology RNA-b 98.8 1.8E-08 3.9E-13 78.1 8.8 66 370-442 3-68 (69)
32 COG1094 Predicted RNA-binding 98.8 9.9E-08 2.1E-12 87.9 13.4 148 41-217 6-167 (194)
33 smart00322 KH K homology RNA-b 98.7 6.4E-08 1.4E-12 75.0 8.8 67 139-212 2-68 (69)
34 COG1094 Predicted RNA-binding 98.7 1.4E-07 3E-12 86.9 10.3 145 283-444 7-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.4 1.1E-06 2.4E-11 76.2 8.1 67 378-444 14-95 (120)
36 cd02395 SF1_like-KH Splicing f 98.3 2.1E-06 4.7E-11 74.4 7.8 67 149-215 15-96 (120)
37 KOG2113 Predicted RNA binding 98.2 8.6E-07 1.9E-11 86.1 4.3 143 282-435 24-173 (394)
38 TIGR02696 pppGpp_PNP guanosine 98.2 9.6E-06 2.1E-10 89.7 10.6 96 107-214 546-642 (719)
39 PRK08406 transcription elongat 98.1 6.1E-06 1.3E-10 73.7 6.2 102 44-175 33-134 (140)
40 KOG2113 Predicted RNA binding 97.9 1.3E-05 2.9E-10 78.0 5.9 142 137-336 23-164 (394)
41 PRK08406 transcription elongat 97.9 4.7E-05 1E-09 68.0 8.8 103 284-405 32-134 (140)
42 KOG0119 Splicing factor 1/bran 97.9 8.6E-05 1.9E-09 76.9 11.2 77 369-445 137-231 (554)
43 TIGR02696 pppGpp_PNP guanosine 97.8 5.1E-05 1.1E-09 84.1 7.7 65 369-444 577-642 (719)
44 KOG0119 Splicing factor 1/bran 97.7 0.00034 7.5E-09 72.5 11.3 77 138-214 136-230 (554)
45 TIGR03591 polynuc_phos polyrib 97.7 0.00011 2.4E-09 82.6 8.2 96 107-213 518-614 (684)
46 KOG0336 ATP-dependent RNA heli 97.6 5.8E-05 1.3E-09 76.7 5.1 64 30-96 34-97 (629)
47 PLN00207 polyribonucleotide nu 97.6 0.00014 3E-09 82.5 7.4 97 107-214 652-750 (891)
48 TIGR01952 nusA_arch NusA famil 97.5 0.00029 6.2E-09 62.8 7.4 102 285-405 34-135 (141)
49 TIGR01952 nusA_arch NusA famil 97.5 0.00011 2.5E-09 65.4 4.8 103 44-176 34-136 (141)
50 COG1185 Pnp Polyribonucleotide 97.5 0.00017 3.6E-09 78.3 6.3 114 90-214 491-616 (692)
51 TIGR03591 polynuc_phos polyrib 97.3 0.00036 7.7E-09 78.6 6.0 65 369-444 550-615 (684)
52 COG0195 NusA Transcription elo 97.1 0.00089 1.9E-08 62.8 6.0 104 44-178 77-180 (190)
53 COG0195 NusA Transcription elo 97.0 0.0033 7.2E-08 58.9 8.2 103 285-407 77-179 (190)
54 COG1185 Pnp Polyribonucleotide 96.9 0.0015 3.3E-08 71.1 5.8 66 370-446 552-618 (692)
55 PRK11824 polynucleotide phosph 96.9 0.0012 2.5E-08 74.7 5.1 97 107-214 521-618 (693)
56 KOG0336 ATP-dependent RNA heli 96.8 0.0021 4.5E-08 65.7 6.1 67 369-443 46-112 (629)
57 PLN00207 polyribonucleotide nu 96.8 0.0011 2.3E-08 75.4 4.3 65 369-444 684-750 (891)
58 KOG1588 RNA-binding protein Sa 96.8 0.006 1.3E-07 59.1 8.5 75 368-442 90-189 (259)
59 KOG1588 RNA-binding protein Sa 96.7 0.0016 3.4E-08 63.1 4.2 39 40-78 89-133 (259)
60 cd02134 NusA_KH NusA_K homolog 96.5 0.0049 1.1E-07 46.8 4.8 36 43-78 25-60 (61)
61 TIGR01953 NusA transcription t 96.4 0.0059 1.3E-07 62.8 5.9 96 52-178 243-339 (341)
62 cd02134 NusA_KH NusA_K homolog 96.3 0.0065 1.4E-07 46.1 4.6 36 370-405 25-60 (61)
63 KOG2814 Transcription coactiva 96.3 0.0046 9.9E-08 61.6 4.5 71 139-215 56-126 (345)
64 PRK12328 nusA transcription el 96.2 0.0079 1.7E-07 61.9 5.7 95 52-178 251-346 (374)
65 KOG2814 Transcription coactiva 96.2 0.0066 1.4E-07 60.5 4.9 71 369-446 56-127 (345)
66 COG5176 MSL5 Splicing factor ( 96.2 0.038 8.2E-07 51.3 9.4 42 368-409 146-193 (269)
67 PRK12328 nusA transcription el 96.2 0.02 4.4E-07 59.0 8.5 97 293-410 251-348 (374)
68 PRK12327 nusA transcription el 96.1 0.0085 1.9E-07 62.0 5.7 96 52-178 245-341 (362)
69 TIGR01953 NusA transcription t 96.1 0.019 4.2E-07 59.1 8.2 93 293-407 243-338 (341)
70 PRK12327 nusA transcription el 96.0 0.022 4.8E-07 59.0 7.8 96 293-408 245-341 (362)
71 PRK04163 exosome complex RNA-b 95.9 0.017 3.6E-07 56.6 6.2 63 372-445 147-210 (235)
72 PRK00468 hypothetical protein; 95.8 0.011 2.3E-07 46.8 3.7 34 39-72 26-59 (75)
73 PRK00106 hypothetical protein; 95.8 0.026 5.7E-07 61.3 7.9 65 369-443 224-290 (535)
74 PRK12329 nusA transcription el 95.8 0.0094 2E-07 62.4 4.2 95 52-177 277-372 (449)
75 TIGR03319 YmdA_YtgF conserved 95.7 0.027 5.8E-07 61.4 7.6 65 369-443 203-269 (514)
76 PRK12329 nusA transcription el 95.7 0.026 5.6E-07 59.2 7.0 95 293-407 277-372 (449)
77 PRK12704 phosphodiesterase; Pr 95.7 0.027 5.9E-07 61.5 7.6 65 369-443 209-275 (520)
78 PRK11824 polynucleotide phosph 95.6 0.0075 1.6E-07 68.2 3.1 64 370-444 554-618 (693)
79 PF14611 SLS: Mitochondrial in 95.6 0.33 7.1E-06 46.7 13.9 131 285-445 27-166 (210)
80 KOG1067 Predicted RNA-binding 95.5 0.028 6.1E-07 59.7 6.4 114 90-215 543-661 (760)
81 COG5176 MSL5 Splicing factor ( 95.4 0.04 8.7E-07 51.2 6.3 44 135-178 143-192 (269)
82 PRK02821 hypothetical protein; 95.4 0.017 3.8E-07 45.8 3.5 34 40-73 28-61 (77)
83 PRK02821 hypothetical protein; 95.3 0.032 6.9E-07 44.3 4.8 35 136-170 27-61 (77)
84 PRK00468 hypothetical protein; 95.3 0.031 6.6E-07 44.2 4.7 35 135-169 25-59 (75)
85 PRK09202 nusA transcription el 95.3 0.018 4E-07 61.8 4.5 94 53-178 246-340 (470)
86 PRK09202 nusA transcription el 95.2 0.044 9.5E-07 58.9 7.0 93 293-408 245-340 (470)
87 COG1837 Predicted RNA-binding 95.1 0.046 1E-06 43.1 4.9 33 136-168 26-58 (76)
88 PF14611 SLS: Mitochondrial in 95.1 0.56 1.2E-05 45.0 13.7 64 141-214 27-90 (210)
89 PRK04163 exosome complex RNA-b 94.8 0.041 8.9E-07 53.9 5.1 63 142-215 147-210 (235)
90 PRK01064 hypothetical protein; 94.7 0.04 8.8E-07 43.9 3.9 33 40-72 27-59 (78)
91 TIGR03319 YmdA_YtgF conserved 94.6 0.14 3.1E-06 55.9 9.1 67 138-214 202-270 (514)
92 PRK01064 hypothetical protein; 94.6 0.079 1.7E-06 42.2 5.2 35 135-169 25-59 (78)
93 PRK12704 phosphodiesterase; Pr 94.5 0.15 3.3E-06 55.7 8.9 66 139-214 209-276 (520)
94 COG1837 Predicted RNA-binding 94.5 0.046 1E-06 43.1 3.6 33 40-72 27-59 (76)
95 PRK00106 hypothetical protein; 94.4 0.19 4E-06 54.8 9.3 67 138-214 223-291 (535)
96 KOG0921 Dosage compensation co 92.6 0.59 1.3E-05 52.9 9.4 28 283-310 935-962 (1282)
97 PF13083 KH_4: KH domain; PDB: 92.6 0.062 1.4E-06 42.3 1.5 34 40-73 26-59 (73)
98 PRK12705 hypothetical protein; 92.5 0.17 3.6E-06 54.9 5.1 38 369-406 197-235 (508)
99 KOG4369 RTK signaling protein 90.4 0.072 1.6E-06 60.9 -0.3 70 372-445 1342-1411(2131)
100 PRK12705 hypothetical protein; 89.7 0.77 1.7E-05 49.8 6.7 66 139-214 197-264 (508)
101 cd02409 KH-II KH-II (K homolo 89.6 0.58 1.2E-05 35.5 4.3 35 42-76 24-58 (68)
102 KOG0921 Dosage compensation co 89.4 1.5 3.3E-05 49.7 8.8 6 490-495 1206-1211(1282)
103 KOG3273 Predicted RNA-binding 89.4 0.18 3.9E-06 46.7 1.4 55 378-444 177-231 (252)
104 KOG1067 Predicted RNA-binding 88.4 0.73 1.6E-05 49.4 5.2 68 366-445 593-661 (760)
105 COG1855 ATPase (PilT family) [ 88.3 0.93 2E-05 47.8 5.8 40 140-179 486-525 (604)
106 cd02409 KH-II KH-II (K homolo 88.0 0.77 1.7E-05 34.8 4.0 35 139-173 24-58 (68)
107 cd02410 archeal_CPSF_KH The ar 87.2 2.6 5.6E-05 37.6 7.2 92 60-179 23-115 (145)
108 PRK13764 ATPase; Provisional 86.9 1.2 2.6E-05 49.5 6.1 43 370-412 481-523 (602)
109 PF13184 KH_5: NusA-like KH do 86.9 0.43 9.4E-06 37.1 2.0 37 371-407 4-46 (69)
110 PF13083 KH_4: KH domain; PDB: 86.7 0.29 6.3E-06 38.5 0.9 34 138-171 27-60 (73)
111 COG5166 Uncharacterized conser 86.5 2.7 5.9E-05 44.7 8.0 152 139-405 448-606 (657)
112 cd02414 jag_KH jag_K homology 86.0 0.8 1.7E-05 36.4 3.1 32 45-76 26-57 (77)
113 KOG3273 Predicted RNA-binding 85.4 0.53 1.1E-05 43.7 2.0 57 148-216 177-233 (252)
114 COG1782 Predicted metal-depend 85.4 2.1 4.6E-05 45.6 6.6 127 57-216 43-174 (637)
115 KOG4369 RTK signaling protein 84.2 0.3 6.6E-06 56.1 -0.1 71 140-214 1340-1410(2131)
116 cd02414 jag_KH jag_K homology 84.1 1.1 2.4E-05 35.5 3.2 34 141-174 25-58 (77)
117 KOG2874 rRNA processing protei 84.0 1.7 3.7E-05 42.6 4.8 51 152-214 161-211 (356)
118 PF13184 KH_5: NusA-like KH do 83.9 0.6 1.3E-05 36.3 1.4 37 142-178 5-47 (69)
119 COG1097 RRP4 RNA-binding prote 83.6 2.6 5.6E-05 40.8 5.9 58 142-210 148-206 (239)
120 KOG3875 Peroxisomal biogenesis 83.2 4 8.8E-05 40.7 7.1 22 504-525 79-100 (362)
121 cd02413 40S_S3_KH K homology R 82.9 1.2 2.6E-05 35.8 2.9 36 45-80 32-67 (81)
122 PF07650 KH_2: KH domain syndr 82.5 0.65 1.4E-05 36.9 1.2 33 44-76 26-58 (78)
123 COG1855 ATPase (PilT family) [ 82.4 0.84 1.8E-05 48.1 2.3 40 371-410 487-526 (604)
124 KOG2874 rRNA processing protei 81.9 2.6 5.6E-05 41.3 5.2 51 382-444 161-211 (356)
125 PRK13764 ATPase; Provisional 81.8 3.1 6.7E-05 46.3 6.5 45 138-182 479-523 (602)
126 COG1097 RRP4 RNA-binding prote 81.0 3.7 8E-05 39.7 5.9 47 372-429 148-194 (239)
127 PF07650 KH_2: KH domain syndr 79.2 0.72 1.6E-05 36.6 0.4 34 140-173 25-58 (78)
128 PRK06418 transcription elongat 79.2 2.5 5.5E-05 38.8 4.0 33 46-79 64-96 (166)
129 cd02413 40S_S3_KH K homology R 78.2 2.7 5.9E-05 33.8 3.5 35 371-405 31-65 (81)
130 PRK06418 transcription elongat 77.3 3.3 7.2E-05 38.0 4.2 36 142-178 63-98 (166)
131 cd02410 archeal_CPSF_KH The ar 74.5 4.6 9.9E-05 36.1 4.1 37 45-81 78-114 (145)
132 TIGR03675 arCOG00543 arCOG0054 71.4 7.6 0.00017 43.7 6.1 96 57-180 37-133 (630)
133 cd02412 30S_S3_KH K homology R 71.1 3.9 8.4E-05 34.9 2.9 31 45-75 63-93 (109)
134 cd02411 archeal_30S_S3_KH K ho 67.8 6.1 0.00013 32.0 3.2 28 45-72 40-67 (85)
135 COG5166 Uncharacterized conser 65.0 11 0.00024 40.3 5.2 130 296-445 392-525 (657)
136 cd02411 archeal_30S_S3_KH K ho 64.9 7.4 0.00016 31.5 3.2 28 372-399 40-67 (85)
137 COG0092 RpsC Ribosomal protein 64.0 6.2 0.00013 38.1 2.9 31 43-73 51-81 (233)
138 cd02412 30S_S3_KH K homology R 63.8 6.3 0.00014 33.6 2.7 29 372-400 63-91 (109)
139 COG0092 RpsC Ribosomal protein 61.9 7.5 0.00016 37.6 3.1 29 370-398 51-79 (233)
140 COG1782 Predicted metal-depend 59.0 27 0.00059 37.6 6.8 39 370-408 99-137 (637)
141 TIGR00436 era GTP-binding prot 53.2 16 0.00035 36.3 4.1 31 369-399 220-251 (270)
142 TIGR00436 era GTP-binding prot 50.0 19 0.00041 35.8 3.9 31 139-169 220-251 (270)
143 TIGR03675 arCOG00543 arCOG0054 49.8 35 0.00077 38.5 6.4 39 370-408 93-131 (630)
144 cd07055 BMC_like_2 Bacterial M 49.8 35 0.00076 25.8 4.2 40 396-440 20-59 (61)
145 COG1159 Era GTPase [General fu 48.3 20 0.00043 36.1 3.6 30 138-167 227-257 (298)
146 COG1159 Era GTPase [General fu 47.8 14 0.0003 37.1 2.5 35 365-399 224-259 (298)
147 PRK15494 era GTPase Era; Provi 47.4 22 0.00048 36.8 4.1 31 369-399 272-303 (339)
148 TIGR03802 Asp_Ala_antiprt aspa 45.3 4.8E+02 0.01 29.1 14.9 62 141-208 304-376 (562)
149 PRK00089 era GTPase Era; Revie 44.7 26 0.00056 35.2 4.0 31 369-399 225-256 (292)
150 PRK15494 era GTPase Era; Provi 44.6 25 0.00055 36.3 4.0 29 140-168 273-302 (339)
151 PRK00089 era GTPase Era; Revie 43.3 28 0.0006 35.0 4.0 29 140-168 226-255 (292)
152 PRK03818 putative transporter; 41.9 3.1E+02 0.0067 30.5 12.2 133 45-207 207-358 (552)
153 TIGR01008 rpsC_E_A ribosomal p 38.3 35 0.00075 32.4 3.5 30 45-74 40-69 (195)
154 CHL00048 rps3 ribosomal protei 38.3 34 0.00073 33.0 3.5 30 44-73 67-96 (214)
155 PRK04191 rps3p 30S ribosomal p 37.7 34 0.00075 32.7 3.4 31 45-75 42-72 (207)
156 KOG1423 Ras-like GTPase ERA [C 37.5 34 0.00073 34.8 3.3 37 364-400 322-359 (379)
157 COG0490 Putative regulatory, l 36.7 28 0.00061 31.7 2.4 61 374-439 92-158 (162)
158 COG1847 Jag Predicted RNA-bind 36.5 32 0.00069 32.7 2.9 37 139-175 90-126 (208)
159 COG1847 Jag Predicted RNA-bind 36.2 25 0.00053 33.4 2.1 34 44-77 92-125 (208)
160 COG1702 PhoH Phosphate starvat 35.6 85 0.0018 32.4 5.9 51 377-439 22-72 (348)
161 TIGR01008 rpsC_E_A ribosomal p 35.4 40 0.00087 31.9 3.4 29 371-399 39-67 (195)
162 PTZ00084 40S ribosomal protein 34.1 41 0.00089 32.5 3.3 32 45-76 46-77 (220)
163 PRK04191 rps3p 30S ribosomal p 33.0 45 0.00097 31.9 3.4 29 372-400 42-70 (207)
164 PF09869 DUF2096: Uncharacteri 33.0 1.2E+02 0.0027 27.7 5.9 57 137-211 110-166 (169)
165 CHL00048 rps3 ribosomal protei 32.6 46 0.001 32.0 3.4 29 371-399 67-95 (214)
166 PTZ00084 40S ribosomal protein 32.4 45 0.00096 32.2 3.2 29 371-399 45-73 (220)
167 KOG1423 Ras-like GTPase ERA [C 32.4 44 0.00096 33.9 3.2 34 137-170 325-359 (379)
168 KOG3973 Uncharacterized conser 31.3 1.2E+02 0.0026 31.1 6.0 12 474-485 365-376 (465)
169 KOG3973 Uncharacterized conser 30.3 1.5E+02 0.0032 30.4 6.5 11 395-405 286-296 (465)
170 PRK15468 carboxysome structura 25.1 1.1E+02 0.0024 25.8 3.9 27 420-446 75-101 (111)
171 PRK04972 putative transporter; 24.7 9.6E+02 0.021 26.7 12.4 64 140-209 303-372 (558)
172 TIGR01009 rpsC_bact ribosomal 23.3 80 0.0017 30.3 3.2 29 45-73 64-92 (211)
173 COG4010 Uncharacterized protei 21.8 2.4E+02 0.0053 25.2 5.5 43 160-213 126-168 (170)
174 PRK15468 carboxysome structura 21.5 2.2E+02 0.0048 24.1 5.0 38 169-215 63-100 (111)
175 PTZ00473 Plasmodium Vir superf 21.2 3.8E+02 0.0082 28.3 7.6 10 64-73 10-19 (420)
176 TIGR01009 rpsC_bact ribosomal 21.0 92 0.002 29.9 3.1 28 372-399 64-91 (211)
177 PF02749 QRPTase_N: Quinolinat 21.0 2.7E+02 0.0059 22.4 5.5 62 378-443 24-85 (88)
No 1
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=4.4e-47 Score=398.77 Aligned_cols=402 Identities=40% Similarity=0.603 Sum_probs=313.9
Q ss_pred cCcCCCCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCC
Q 009012 5 RNSYGKRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPG 84 (546)
Q Consensus 5 ~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~ 84 (546)
|....++....+...+++..+++...++.... ..+...++||||+.+.+|.||||+|++||+||.+|.++|+|.+..++
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~ 84 (485)
T KOG2190|consen 6 RGLPRPKNSTTSNVGDNGSIKRPSLGDPVIST-GPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPG 84 (485)
T ss_pred ccCccccCCCcccccCCCcccccCCCCCcccC-CCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCC
Confidence 44555566666666566666665555554333 33334449999999999999999999999999999999999999999
Q ss_pred CcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhh---cCCC--C-CCCCCceEEEEEeeCCceeEEeccC
Q 009012 85 SEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEEL---RGDE--D-SDGGHQVTAKLLVPSDQIGCVIGKG 158 (546)
Q Consensus 85 ~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~---~~~~--~-~~~~~~~~~~llVp~~~vg~IIGk~ 158 (546)
|+||+|+|+|...+ ..++.+++|++++++.+..... .... . +.....++++||||+++||+||||+
T Consensus 85 c~eRIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~ 156 (485)
T KOG2190|consen 85 CPERIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKG 156 (485)
T ss_pred CCcceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccC
Confidence 99999999997322 1688899999999998886321 1111 1 1222368999999999999999999
Q ss_pred chHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcchhhcccccCCCCCCCCCC
Q 009012 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLV 238 (546)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~ 238 (546)
|+.||+|+++|||+|+|.++ .+|. +++|.|+|.|.+++|.+|+.+|..+|++++.+......+... |.. .
T Consensus 157 G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~--y~P----~ 226 (485)
T KOG2190|consen 157 GSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIP--YRP----S 226 (485)
T ss_pred cHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCccc--CCC----c
Confidence 99999999999999999987 8887 588999999999999999999999999976553222211111 000 0
Q ss_pred CCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEE
Q 009012 239 GPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIK 318 (546)
Q Consensus 239 ~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~ 318 (546)
-+..++ +...++. ..+ .+.++.....+.++..++.+|.+.++.|||+++..|+.|+.++++.|.
T Consensus 227 ~~~~~~-------~~~s~~~-------~~~--~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~ 290 (485)
T KOG2190|consen 227 ASQGGP-------VLPSTAQ-------TSP--DAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASIS 290 (485)
T ss_pred ccccCc-------ccccccc-------CCc--ccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceE
Confidence 000000 0000000 000 112222334556788899999999999999999999999999999999
Q ss_pred ecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHh
Q 009012 319 VDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (546)
Q Consensus 319 i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~ 398 (546)
+.+..++ |+++++..+..++..++++++++++++.+.+...... ...++.+|+||.+++||||||+|.+|.+||+.
T Consensus 291 v~~~~~~---~~i~~s~~e~~~~~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~ 366 (485)
T KOG2190|consen 291 VGDSRTD---RIVTISARENPEDRYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQR 366 (485)
T ss_pred eccccCc---ceeeeccccCcccccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHh
Confidence 9987654 9999999999999999999999999999988877665 77899999999999999999999999999999
Q ss_pred cCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhcccc
Q 009012 399 TKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRANLFD 448 (546)
Q Consensus 399 tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~~ 448 (546)
|||.|+|..+++. ...++++|+|+|+..+...|..++..++......
T Consensus 367 tgA~I~I~~~~~~---~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~ 413 (485)
T KOG2190|consen 367 TGASISILNKEEV---SGVREALVQITGMLREDLLAQYLIRARLSAPKSS 413 (485)
T ss_pred cCCceEEcccccc---CCcceeEEEecchhHHHHhhhhhcccccccCccC
Confidence 9999999887653 2467899999999999999999998888766543
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=7.4e-44 Score=367.34 Aligned_cols=334 Identities=20% Similarity=0.375 Sum_probs=253.8
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHH
Q 009012 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (546)
Q Consensus 41 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~ 120 (546)
..++.++.||.++|++||||+|+.|..|+.+++|+|+|.....+..+|.|.++|.++++ +.|- +++
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v-------------~~aK-~li 117 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENV-------------EVAK-QLI 117 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccH-------------HHHH-Hhh
Confidence 44568899999999999999999999999999999998777667789999999999984 2232 222
Q ss_pred HHHHHhhhcCC--CCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCH
Q 009012 121 DRVIAEELRGD--EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (546)
Q Consensus 121 ~~i~~~~~~~~--~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~ 198 (546)
..++....... .+.-....++..|+||.+.||.||||+|+|||.|++++||++.+..+..... ..++.+.|+|++
T Consensus 118 ~evv~r~~~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp 194 (600)
T KOG1676|consen 118 GEVVSRGRPPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP 194 (600)
T ss_pred hhhhhccCCCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence 32332221110 1112246689999999999999999999999999999999999998765432 578999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009012 199 SVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDD 278 (546)
Q Consensus 199 ~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~ 278 (546)
+.|+.|..+|.++|++.... .+..++. ++. +
T Consensus 195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~~-------------------~g~---~---------------- 225 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDDE-----------VPGSGGH-------------------AGV---R---------------- 225 (600)
T ss_pred HHHHHHHHHHHHHHHhcccC-----------CCccccc-------------------cCc---C----------------
Confidence 99999999999999863211 1111000 000 0
Q ss_pred CCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCC-CCCceEEEEecCcchhhhchHHHHHHHHhcCcc
Q 009012 279 LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSST-EGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC 357 (546)
Q Consensus 279 ~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~-~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~ 357 (546)
.....+.+|.||...||.||||+|++||+|+.+||++|+|.+.+. .+.||++.|.|...........+.+++......
T Consensus 226 -~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~d~ie~Aa~lI~eii~~~~~~ 304 (600)
T KOG1676|consen 226 -GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTVDQIEHAAELINEIIAEAEAG 304 (600)
T ss_pred -ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCHHHHHHHHHHHHHHHHHHhcc
Confidence 011238899999999999999999999999999999999987654 678999999997543222233333333321111
Q ss_pred ccccccccCCcce--eEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHH
Q 009012 358 SEKIERDSGLISF--TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (546)
Q Consensus 358 ~~~~~~~~~~~~~--~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~ 435 (546)
.. ..-..+.... ...|.||.+.||+||||+|++||.|.++|||++.+.+. |+..+..+++|+|.|++.+|+.|.
T Consensus 305 ~~-~~~~~G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~QIdhAk 380 (600)
T KOG1676|consen 305 AG-GGMGGGAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKRQIDHAK 380 (600)
T ss_pred CC-CCcCCCCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcccchHHH
Confidence 00 0000122223 78899999999999999999999999999999999764 445677899999999999999999
Q ss_pred HHHHHHHHhc
Q 009012 436 IQVMTRLRAN 445 (546)
Q Consensus 436 ~~I~~~l~~~ 445 (546)
.||.+++...
T Consensus 381 ~LIr~kvg~~ 390 (600)
T KOG1676|consen 381 QLIRDKVGDI 390 (600)
T ss_pred HHHHHHhccc
Confidence 9999999874
No 3
>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=4.2e-42 Score=337.77 Aligned_cols=365 Identities=22% Similarity=0.363 Sum_probs=273.5
Q ss_pred ccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC-CCCCCcceEEEEecCCccccccccCcccCCHHHHH
Q 009012 37 IIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDA 115 (546)
Q Consensus 37 ~~~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a 115 (546)
.....+..+|+|||..+||.||||.|.|||.|-..|.|+|.|.. ...+..|++|+|-+.+|. +.+|
T Consensus 193 ~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~A 259 (584)
T KOG2193|consen 193 KQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKA 259 (584)
T ss_pred cccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHH
Confidence 34477888999999999999999999999999999999999964 456889999999999998 4789
Q ss_pred HHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEE
Q 009012 116 LFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQIS 195 (546)
Q Consensus 116 ~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~ 195 (546)
|.+|++.+..+.... .....+.+++|.++.+||+||||.|.+||+|+.+||++|.|++-.++.. .+.+|+++|.
T Consensus 260 c~~ILeimqkEA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~--ynpERTItVk 333 (584)
T KOG2193|consen 260 CKMILEIMQKEAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSL--YNPERTITVK 333 (584)
T ss_pred HHHHHHHHHHhhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcc--cCccceEEec
Confidence 999998766554322 2336778999999999999999999999999999999999998766554 3679999999
Q ss_pred cCHHHHHHHHHHHHHHHhcCCCCcchhhcccccCCCCCCCCCCCCCC--CCCcccCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009012 196 GEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTA--ATPIVGIAPLMGPYGGYKGDTAGDWSRSLYS 273 (546)
Q Consensus 196 G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~p~~--g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~ 273 (546)
|+.|+|..|..+|+.+|+++..++.. +-+..-..+. .++.|.. ++....+.|+- ..+.-+....++.++
T Consensus 334 GsiEac~~AE~eImkKlre~yEnDl~--a~s~q~~l~P--~l~~~~l~~f~ssS~~~~Ph----~~Ps~v~~a~p~~~~- 404 (584)
T KOG2193|consen 334 GSIEACVQAEAEIMKKLRECYENDLA--AMSLQCHLPP--GLNLPALGLFPSSSAVSPPH----FPPSPVTFASPYPLF- 404 (584)
T ss_pred ccHHHHHHHHHHHHHHHHHHHhhhHH--HhhccCCCCc--ccCccccCCCCcccccCCCC----CCCCccccCCCchhh-
Confidence 99999999999999999998766521 1111111111 1111111 01111111100 000000000010111
Q ss_pred CCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCC-CCCCceEEEEecCcchhhhchHHHHHHHH
Q 009012 274 APRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS-TEGDDCLITVSSKEFFEDTLSATIEAVVR 352 (546)
Q Consensus 274 ~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~-~~~~~rvi~I~G~~~~~~~~~~~~~a~~~ 352 (546)
........+++.||...+|.|||++|.+||+|...+||.|+|.... ++..+|+++|+|.+ ++.++
T Consensus 405 ----hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp----------eaqfK 470 (584)
T KOG2193|consen 405 ----HQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP----------EAQFK 470 (584)
T ss_pred ----hcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh----------HHHHh
Confidence 1122455889999999999999999999999999999999998754 55688999999964 34455
Q ss_pred hcCcccccccc-----ccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcC
Q 009012 353 LQPRCSEKIER-----DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427 (546)
Q Consensus 353 ~~~~~~~~~~~-----~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~ 427 (546)
.+.++..++.. +.....+.+.+.||...+|+||||||.+++||+..|+|-+.|+++. .|. +.+..+|.|.|.
T Consensus 471 AQgrifgKikEenf~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd--End~vivriiGh 547 (584)
T KOG2193|consen 471 AQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD--ENDQVIVRIIGH 547 (584)
T ss_pred hhhhhhhhhhhhccCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC--ccceeeeeeech
Confidence 55554444332 2234467888999999999999999999999999999999997654 453 455567999999
Q ss_pred HHHHHHHHHHHHHHHHhcc
Q 009012 428 LDLAKDALIQVMTRLRANL 446 (546)
Q Consensus 428 ~~~v~~A~~~I~~~l~~~~ 446 (546)
..+...|...|.+.|.+..
T Consensus 548 fyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 548 FYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred hhcchHHHHHHHHHHHHHH
Confidence 9999999999999998765
No 4
>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=1.1e-33 Score=263.66 Aligned_cols=353 Identities=19% Similarity=0.275 Sum_probs=223.0
Q ss_pred CCCCCCCCCCCCCCCccccCCCCCCCcccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceE
Q 009012 10 KRSHSQTDYADHGPNKRRYTGDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERV 89 (546)
Q Consensus 10 ~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~erv 89 (546)
||.|+..+.++.+ +|...| -+..++....+.+|||+.++.+|.||||+|++||+|+.+++|.|.|.+. ..+||+
T Consensus 19 ~~~~~~e~g~~~g---krp~~d-~~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri 92 (390)
T KOG2192|consen 19 ETFPNTETGGEFG---KRPAED-MEEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERI 92 (390)
T ss_pred hcCCCCccccccc---CCcchh-hHHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCcee
Confidence 5556655543332 333333 3666778888999999999999999999999999999999999999887 788999
Q ss_pred EEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhc
Q 009012 90 VTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 90 v~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~t 169 (546)
++|+...+. +-+-|++++..+.+. + .....+.++|||+.+++|.|||++|++||+|++++
T Consensus 93 ~tisad~~t-------------i~~ilk~iip~lee~-f------~~~~pce~rllihqs~ag~iigrngskikelrekc 152 (390)
T KOG2192|consen 93 LTISADIET-------------IGEILKKIIPTLEEG-F------QLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKC 152 (390)
T ss_pred EEEeccHHH-------------HHHHHHHHhhhhhhC-C------CCCCchhhhhhhhhhhccceecccchhHHHHHHhh
Confidence 999976332 234444444444221 1 34567999999999999999999999999999999
Q ss_pred CceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcchhhcccccCC----CCCCCC-CCC-CCCC
Q 009012 170 GAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNS----HSSSGS-LVG-PTAA 243 (546)
Q Consensus 170 ga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~----~~~gg~-~~~-p~~g 243 (546)
.|+++|... -|..++||+|.|.|.+..|..+++.|++.|.+.|.+..... +.++. |..||. |+. -.++
T Consensus 153 sarlkift~----c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~p--y~p~fyd~t~dyggf~M~f~d~pg 226 (390)
T KOG2192|consen 153 SARLKIFTE----CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQP--YDPNFYDETYDYGGFTMMFDDRPG 226 (390)
T ss_pred hhhhhhhhc----cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCc--CCccccCcccccCCceeecCCCCC
Confidence 999999864 46679999999999999999999999999999887754321 12211 222221 111 0000
Q ss_pred -----C--CcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCe
Q 009012 244 -----T--PIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAA 316 (546)
Q Consensus 244 -----~--~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~ 316 (546)
+ +..+.+|...++.+ .+-++|..= +.+--.
T Consensus 227 ~pgpapqrggqgpp~~~~sdlm---------------------------------------ay~r~GrpG----~rydg~ 263 (390)
T KOG2192|consen 227 RPGPAPQRGGQGPPPPRGSDLM---------------------------------------AYDRRGRPG----DRYDGM 263 (390)
T ss_pred CCCCCCCCCCCCCCCCCccccc---------------------------------------eeccCCCCC----cccccc
Confidence 0 00111111111110 000000000 000000
Q ss_pred EEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccccCCcceeEEEEEcCCcceeEEcCCChhHHHHH
Q 009012 317 IKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMR 396 (546)
Q Consensus 317 I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~ 396 (546)
+.|...... ...+-+-..++ +...+.+..-.--..-..-....-.+.+.+..|..+.||.++-|.||||+|+.|++|+
T Consensus 264 vdFs~detw-~saidtw~~Se-wqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir 341 (390)
T KOG2192|consen 264 VDFSADETW-PSAIDTWSPSE-WQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIR 341 (390)
T ss_pred ccccccccC-CCcCCCcCccc-cccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhh
Confidence 111111000 00000000000 0000000000000000000000011233456889999999999999999999999999
Q ss_pred HhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009012 397 RLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 397 ~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 444 (546)
+++||.|+|... ..++.+|.++|+|+.++++.|+.|++..++.
T Consensus 342 ~esGA~Ikidep-----leGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 342 HESGASIKIDEP-----LEGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred hccCceEEecCc-----CCCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 999999999653 2367889999999999999999999999875
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.97 E-value=5.8e-29 Score=257.32 Aligned_cols=242 Identities=26% Similarity=0.420 Sum_probs=183.8
Q ss_pred CCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCC--CCCCcceEEEEecCCccccccccCcccCCHHHHHH
Q 009012 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET--VPGSEERVVTVYSASDETNAFEDGDKFVSPAQDAL 116 (546)
Q Consensus 39 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~--~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~ 116 (546)
++..++..|+||..++|+||||+|++||+|++.+||++.+... ......+.+.|+|.++.+ +.|.
T Consensus 135 ~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~a~ 201 (600)
T KOG1676|consen 135 GSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQAK 201 (600)
T ss_pred CccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HHHH
Confidence 3677899999999999999999999999999999999987543 222256889999998873 4555
Q ss_pred HHHHHHHHHhhhcCCC-----CCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCce
Q 009012 117 FKVHDRVIAEELRGDE-----DSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDEL 191 (546)
Q Consensus 117 ~~i~~~i~~~~~~~~~-----~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~ 191 (546)
.++++.|.++.-.... ........+++|.||.+.||.||||+|++||+|+.+|||||+|.++++ | .+.+|.
T Consensus 202 ~lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~ 277 (600)
T KOG1676|consen 202 QLVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERP 277 (600)
T ss_pred HHHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccce
Confidence 5666655533211111 112233458999999999999999999999999999999999998754 3 378999
Q ss_pred EEEEcCHHHHHHHHHHHHHHHhcCCCCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCC
Q 009012 192 VQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSL 271 (546)
Q Consensus 192 v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~ 271 (546)
+.|.|+.+.|..|.++|.++|++..... .+ + + +|.
T Consensus 278 ~~IiG~~d~ie~Aa~lI~eii~~~~~~~----------~~---~-~----------------------------~~G--- 312 (600)
T KOG1676|consen 278 AQIIGTVDQIEHAAELINEIIAEAEAGA----------GG---G-M----------------------------GGG--- 312 (600)
T ss_pred eeeecCHHHHHHHHHHHHHHHHHHhccC----------CC---C-c----------------------------CCC---
Confidence 9999999999999999999998742110 00 0 0 000
Q ss_pred CCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCC--CCCCceEEEEecCcchhhhchHHHHH
Q 009012 272 YSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSS--TEGDDCLITVSSKEFFEDTLSATIEA 349 (546)
Q Consensus 272 ~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~--~~~~~rvi~I~G~~~~~~~~~~~~~a 349 (546)
.| ..-..+.+.||.+.+|+|||++|++||.|.+++||++.+.+.. .+..+++++|.|.+.-.+.....++.
T Consensus 313 --~P-----~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~~QIdhAk~LIr~ 385 (600)
T KOG1676|consen 313 --AP-----GLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDKRQIDHAKQLIRD 385 (600)
T ss_pred --Cc-----cceeeEEEeccccccccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCcccchHHHHHHHH
Confidence 00 0011678999999999999999999999999999999999873 23478999999987544443334333
No 6
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=4.8e-29 Score=245.86 Aligned_cols=243 Identities=23% Similarity=0.382 Sum_probs=190.8
Q ss_pred CceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 009012 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPS 217 (546)
Q Consensus 138 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~ 217 (546)
....+|+|||..++|.||||.|+|||+|...|-|+|.|..+++. +..|+.|+|.+++|...+|+++|+++|.+...
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~----Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENA----GAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccC----CcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 45779999999999999999999999999999999999987653 46899999999999999999999999987532
Q ss_pred CcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccc
Q 009012 218 RSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGG 297 (546)
Q Consensus 218 ~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~ 297 (546)
++ ....++.++++-.+.++|+
T Consensus 273 ~~-----------------------------------------------------------k~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 273 DD-----------------------------------------------------------KVAEEIPLKILAHNNLVGR 293 (584)
T ss_pred cc-----------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence 21 1234678899999999999
Q ss_pred cccCCchhHHHHHhhhCCeEEecCCC---CCCCceEEEEecCc-chh-------hhchHHHHHHHH---hcC----cccc
Q 009012 298 VIGKGGAIINQIRQESGAAIKVDSSS---TEGDDCLITVSSKE-FFE-------DTLSATIEAVVR---LQP----RCSE 359 (546)
Q Consensus 298 iIGk~G~~Ik~i~~~sga~I~i~~~~---~~~~~rvi~I~G~~-~~~-------~~~~~~~~a~~~---~~~----~~~~ 359 (546)
+|||.|.+||+|+++||++|.|.+-. .-.+||+|++.|.- .+. +.+.++.|.-++ ++. .++-
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~ 373 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNL 373 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCc
Confidence 99999999999999999999998742 23479999999941 111 111222222221 111 0000
Q ss_pred c----------cccc-----------------cCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCC
Q 009012 360 K----------IERD-----------------SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (546)
Q Consensus 360 ~----------~~~~-----------------~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P 412 (546)
. +..+ .....-..+|.||...+|.||||+|..||.|.+.+||.|+|...+
T Consensus 374 ~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE--- 450 (584)
T KOG2193|consen 374 PALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE--- 450 (584)
T ss_pred cccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC---
Confidence 0 0000 011335678999999999999999999999999999999997643
Q ss_pred CCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhccc
Q 009012 413 KIASEDDEMVQISGDLDLAKDALIQVMTRLRANLF 447 (546)
Q Consensus 413 ~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 447 (546)
.++..+|||+|+|++++.-+|.-.|..+|+++.|
T Consensus 451 -~pdvseRMViItGppeaqfKAQgrifgKikEenf 484 (584)
T KOG2193|consen 451 -IPDVSERMVIITGPPEAQFKAQGRIFGKIKEENF 484 (584)
T ss_pred -CCCcceeEEEecCChHHHHhhhhhhhhhhhhhcc
Confidence 4467899999999999999999999999999865
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=3.3e-26 Score=220.05 Aligned_cols=236 Identities=24% Similarity=0.374 Sum_probs=170.8
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC---CCCCCcceEEEEecCCccccccccCcccCCHHHHHHH
Q 009012 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE---TVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALF 117 (546)
Q Consensus 41 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~---~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~ 117 (546)
..+.++||||+..+|+||||+|++|.+|+.+|||+|++++ ..|+++||||.|.|+.+++ ..-+.
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai-------------~av~e 103 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEAL-------------NAVHE 103 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHH-------------HHHHH
Confidence 4489999999999999999999999999999999999974 4899999999999996552 22333
Q ss_pred HHHHHHHHhhhcCCC-CC-----CCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEec-CCCCCcccCCCCc
Q 009012 118 KVHDRVIAEELRGDE-DS-----DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK-DEHLPSCALRSDE 190 (546)
Q Consensus 118 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~-~~~~p~~~~~~dr 190 (546)
.|.++|.+....... .+ ..+..-.++|+||++.+|.||||+|.+||.|+++++|-|+|++ ++ ....-.+|
T Consensus 104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkp---t~~sLqer 180 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKP---TGISLQER 180 (402)
T ss_pred HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCC---CCccceeE
Confidence 455555543221111 11 1112235999999999999999999999999999999999984 32 22235799
Q ss_pred eEEEEcCHHHHHHHHHHHHHHHhcCCCCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCC
Q 009012 191 LVQISGEASVVKKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRS 270 (546)
Q Consensus 191 ~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~ 270 (546)
+|++.|++++..+|+.+|+++|.++|...+++..++. +-.|+.- ...|...+|.... +
T Consensus 181 vvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpva----------NsnPtGspya~~~-~-------- 238 (402)
T KOG2191|consen 181 VVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVA----------NSNPTGSPYAYQA-H-------- 238 (402)
T ss_pred EEEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCccc----------ccCCCCCCCCCCC-c--------
Confidence 9999999999999999999999999877665442221 1111111 1111111221111 0
Q ss_pred CCCCCCCCCCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCC
Q 009012 271 LYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSS 322 (546)
Q Consensus 271 ~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~ 322 (546)
..+.......-++..++|..-|.++.++-.|-.-+|+.+.++..
T Consensus 239 --------~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 239 --------VLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred --------cccccchhhccccccccccccccccccceeeecccccceeeccc
Confidence 01122355677889999999999999999999999998888764
No 8
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.90 E-value=1.2e-22 Score=190.02 Aligned_cols=173 Identities=26% Similarity=0.398 Sum_probs=142.7
Q ss_pred ccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCcccccc
Q 009012 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI 361 (546)
Q Consensus 282 ~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~ 361 (546)
..+.+++++..+.+|.||||+|++||.|+.+++|+|.|+++. .++++++|++.+. ...+-+..+.+.+.+.+
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~--~peri~tisad~~------ti~~ilk~iip~lee~f 117 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSS--GPERILTISADIE------TIGEILKKIIPTLEEGF 117 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCC--CCceeEEEeccHH------HHHHHHHHHhhhhhhCC
Confidence 457999999999999999999999999999999999999865 4689999998642 12223334445554433
Q ss_pred ccccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHH
Q 009012 362 ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTR 441 (546)
Q Consensus 362 ~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~ 441 (546)
.. ...+..+|+|+.+++|.|||++|++|||||++..|+++|... +.| ++++|+|.|.|.+..|..+++.|++.
T Consensus 118 ~~---~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~ 190 (390)
T KOG2192|consen 118 QL---PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDL 190 (390)
T ss_pred CC---CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHH
Confidence 22 235899999999999999999999999999999999999764 334 68999999999999999999999999
Q ss_pred HHhccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009012 442 LRANLFDREGAVSTFVPVLPYIPVSENGSDGLNYESRD 479 (546)
Q Consensus 442 l~~~~~~~~~~~~~~~~~~~y~p~~~~~~~~~~y~~~~ 479 (546)
|.+.++ ++...||+|..+++. ..||++.
T Consensus 191 i~e~pi--------kgsa~py~p~fyd~t--~dyggf~ 218 (390)
T KOG2192|consen 191 ISESPI--------KGSAQPYDPNFYDET--YDYGGFT 218 (390)
T ss_pred hhcCCc--------CCcCCcCCccccCcc--cccCCce
Confidence 998554 778889999998865 5677755
No 9
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.88 E-value=8.3e-22 Score=189.82 Aligned_cols=251 Identities=24% Similarity=0.338 Sum_probs=179.9
Q ss_pred CCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009012 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (546)
Q Consensus 137 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 216 (546)
+..+.++||||+..+|.||||+|++|.+|+.+|||+|++++..++.+ ..+||+|.|+|+.++|...+..|.++|++.+
T Consensus 36 ~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyP--GTTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 36 DGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYP--GTTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred CCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCC--CccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 34489999999999999999999999999999999999998655433 4899999999999999999999999999864
Q ss_pred CCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCccc
Q 009012 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (546)
Q Consensus 217 ~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g 296 (546)
..... +.+.+++.. ....-.++++||+...|
T Consensus 114 ~~~~k----------------------------------------------~v~~~~pqt---~~r~kqikivvPNstag 144 (402)
T KOG2191|consen 114 QAVAK----------------------------------------------PVDILQPQT---PDRIKQIKIVVPNSTAG 144 (402)
T ss_pred HhhcC----------------------------------------------CccccCCCC---ccccceeEEeccCCccc
Confidence 32210 000111111 11223589999999999
Q ss_pred ccccCCchhHHHHHhhhCCeEEecCCCCC---CCceEEEEecCcchhhhchHHHHHHHH-hc--Cc---c-cccc-----
Q 009012 297 GVIGKGGAIINQIRQESGAAIKVDSSSTE---GDDCLITVSSKEFFEDTLSATIEAVVR-LQ--PR---C-SEKI----- 361 (546)
Q Consensus 297 ~iIGk~G~~Ik~i~~~sga~I~i~~~~~~---~~~rvi~I~G~~~~~~~~~~~~~a~~~-~~--~~---~-~~~~----- 361 (546)
.||||+|.+||.|+++++|.|+|.+..+. -.+|++++.|+..-. ..+++.++. ++ +. | ....
T Consensus 145 ~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~e~~---~~A~~~IL~Ki~eDpqs~scln~sya~vsG 221 (402)
T KOG2191|consen 145 MIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEPEQN---MKAVSLILQKIQEDPQSGSCLNISYANVSG 221 (402)
T ss_pred ceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCHHHH---HHHHHHHHHHhhcCCcccceeccchhcccC
Confidence 99999999999999999999999965433 378999999964211 112222221 11 00 0 0000
Q ss_pred --------------ccccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcC
Q 009012 362 --------------ERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD 427 (546)
Q Consensus 362 --------------~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~ 427 (546)
.........+....|+...+|..-|.+|.++-.|-..+|+.|.+.+..+.-. +...+ +-+.|.
T Consensus 222 pvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m~--g~gy~-~n~~g~ 298 (402)
T KOG2191|consen 222 PVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTMA--GYGYN-TNILGL 298 (402)
T ss_pred cccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeecccccccc--ccccc-ccccch
Confidence 0001123345667899999999999999999999999999999987654221 23333 667788
Q ss_pred HHHHHHHHHHHHHHHHh
Q 009012 428 LDLAKDALIQVMTRLRA 444 (546)
Q Consensus 428 ~~~v~~A~~~I~~~l~~ 444 (546)
+-++..|-.+|..++..
T Consensus 299 ~ls~~aa~g~L~~~~~~ 315 (402)
T KOG2191|consen 299 GLSILAAEGVLAAKVAS 315 (402)
T ss_pred hhhhhhhhhHHHHhhcc
Confidence 87777776666555543
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.87 E-value=4.3e-21 Score=202.52 Aligned_cols=173 Identities=38% Similarity=0.597 Sum_probs=142.1
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCcccccccc
Q 009012 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (546)
Q Consensus 284 ~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (546)
.++|++|+...+|.||||+|..||+||.++.++|+|.....++.+|+++|+|. ..+...+.+.+++.+++.++...++.
T Consensus 43 ~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~-~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 43 LTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGN-RVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred ceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecc-cccccCCchHHHHHHHHHHHhhcccc
Confidence 34899999999999999999999999999999999999888899999999994 22224455677777766655543221
Q ss_pred ----------ccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHH
Q 009012 364 ----------DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKD 433 (546)
Q Consensus 364 ----------~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~ 433 (546)
+.....++.+|+||..++|+||||+|++||+|+++|||+|+|..+ .+|. .++|.|+|.|++++|.+
T Consensus 122 d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~ 197 (485)
T KOG2190|consen 122 DDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKK 197 (485)
T ss_pred cccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHH
Confidence 111235889999999999999999999999999999999999875 7785 67889999999999999
Q ss_pred HHHHHHHHHHhccccccCCCCCCCCCCCCCC
Q 009012 434 ALIQVMTRLRANLFDREGAVSTFVPVLPYIP 464 (546)
Q Consensus 434 A~~~I~~~l~~~~~~~~~~~~~~~~~~~y~p 464 (546)
|+.+|..+|.+..-. ..+.+....+|.|
T Consensus 198 al~~Is~~L~~~~~~---~~~~~~st~~y~P 225 (485)
T KOG2190|consen 198 ALVQISSRLLENPPR---SPPPLVSTIPYRP 225 (485)
T ss_pred HHHHHHHHHHhcCCc---CCCCCCCcccCCC
Confidence 999999999987532 2334556678888
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=99.55 E-value=3.6e-14 Score=131.62 Aligned_cols=137 Identities=22% Similarity=0.262 Sum_probs=95.1
Q ss_pred EEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEe---cCCccccccccCcccCCHHHHHHHHHHHHH
Q 009012 47 YLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY---SASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 47 ilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~---G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i 123 (546)
|.||.+.+|.|||++|++|+.|+++|+|+|.|.+. +..|.|+ +.++. +.+|...+.. +
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~-i 62 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKA-I 62 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHH-H
Confidence 56899999999999999999999999999999653 3578883 22222 2333333222 1
Q ss_pred HHhhhcCCCC-CCCCCceEEE-EEeeC---------CceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceE
Q 009012 124 IAEELRGDED-SDGGHQVTAK-LLVPS---------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELV 192 (546)
Q Consensus 124 ~~~~~~~~~~-~~~~~~~~~~-llVp~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v 192 (546)
... +..+.. .-....+++. +-|+. ..+|+|||++|++++.|++.|||+|.|. +..|
T Consensus 63 ~~g-f~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~------------~~~v 129 (172)
T TIGR03665 63 GRG-FSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY------------GKTV 129 (172)
T ss_pred HcC-CCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc------------CCEE
Confidence 110 000000 0011122222 23333 3689999999999999999999999984 3579
Q ss_pred EEEcCHHHHHHHHHHHHHHHhcC
Q 009012 193 QISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 193 ~I~G~~~~V~~A~~~I~~~l~~~ 215 (546)
.|.|++++++.|..+|.+++...
T Consensus 130 ~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 130 GIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EEECCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999554
No 12
>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=99.52 E-value=4e-14 Score=131.31 Aligned_cols=138 Identities=21% Similarity=0.259 Sum_probs=94.1
Q ss_pred EEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEE---ecCcchhhhchHHHHHHHHhcCccccccccc
Q 009012 288 LVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV---SSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 288 v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I---~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
+.||.+.++.|||++|++|++|+++|||+|.++.. +..+.| ++.......+...+.++.+-++ .+..-.-
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~--~e~A~~l 74 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAVMKAREVVKAIGRGFS--PEKALKL 74 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHHHHHHHHHHHHHcCCC--HHHHHHh
Confidence 57899999999999999999999999999999963 245666 2222111111222222222111 0000000
Q ss_pred cCCcceeEEEEEcC---------CcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHH
Q 009012 365 SGLISFTTRLLVPT---------SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDAL 435 (546)
Q Consensus 365 ~~~~~~~~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~ 435 (546)
.++...-.-+.|+. ..+|.|||++|++++.|+..|||+|.|.. ..|.|.|++++++.|.
T Consensus 75 ~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~~~A~ 142 (172)
T TIGR03665 75 LDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQVQIAR 142 (172)
T ss_pred cCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHHHHHH
Confidence 11111222234443 47899999999999999999999999942 5899999999999999
Q ss_pred HHHHHHHHh
Q 009012 436 IQVMTRLRA 444 (546)
Q Consensus 436 ~~I~~~l~~ 444 (546)
.+|.++|..
T Consensus 143 ~~i~~li~~ 151 (172)
T TIGR03665 143 EAIEMLIEG 151 (172)
T ss_pred HHHHHHHcC
Confidence 999998854
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.52 E-value=1.5e-13 Score=128.32 Aligned_cols=141 Identities=21% Similarity=0.221 Sum_probs=97.8
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEe----cCCccccccccCcccCCHHHHHHHH
Q 009012 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVY----SASDETNAFEDGDKFVSPAQDALFK 118 (546)
Q Consensus 43 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~----G~~e~~~~~e~~~~~v~~a~~a~~~ 118 (546)
+...+.||.+.++.|||++|++|+.|+++|||+|.|.+. +..|.|+ +.++. +.+|...
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~-------------i~kA~~~ 64 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLA-------------VLKARDI 64 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHH-------------HHHHHHH
Confidence 467899999999999999999999999999999999653 3577886 33222 2333333
Q ss_pred HHHHHHHhhhcCCCC-CCCCCceEEEE-Ee----e-----CCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCC
Q 009012 119 VHDRVIAEELRGDED-SDGGHQVTAKL-LV----P-----SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALR 187 (546)
Q Consensus 119 i~~~i~~~~~~~~~~-~~~~~~~~~~l-lV----p-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~ 187 (546)
+.. +... +..+.. ......+..++ -| + ...+|+|||++|++++.|++.|||+|.|..
T Consensus 65 I~a-i~~g-f~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~---------- 132 (180)
T PRK13763 65 VKA-IGRG-FSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG---------- 132 (180)
T ss_pred HHH-HhcC-CCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----------
Confidence 322 1110 000000 00011122221 11 1 136899999999999999999999999853
Q ss_pred CCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009012 188 SDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 188 ~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (546)
+.|.|.|++++++.|...|.++++..
T Consensus 133 --~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 --KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred --CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 34999999999999999999999664
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.50 E-value=1.7e-13 Score=128.00 Aligned_cols=142 Identities=19% Similarity=0.219 Sum_probs=95.7
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEe----cCcchhhhchHHHHHHHHhcCcccc
Q 009012 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVS----SKEFFEDTLSATIEAVVRLQPRCSE 359 (546)
Q Consensus 284 ~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~----G~~~~~~~~~~~~~a~~~~~~~~~~ 359 (546)
+...+.||.+.++.|||++|++|+.|+++|||+|.++.. +..|.|. +.......+...++++..-++ ..+
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~-~e~ 76 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS-PEK 76 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC-HHH
Confidence 467899999999999999999999999999999999963 2455665 222111111223333322111 000
Q ss_pred ccccccCCcceeEEEEEc---------CCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHH
Q 009012 360 KIERDSGLISFTTRLLVP---------TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL 430 (546)
Q Consensus 360 ~~~~~~~~~~~~~~l~VP---------~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~ 430 (546)
.+ ...++...-.-+.|. ...+|.|||++|++++.|++.|||+|.|.. ..|.|.|++++
T Consensus 77 A~-~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~~~ 143 (180)
T PRK13763 77 AL-RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDPEQ 143 (180)
T ss_pred HH-HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCHHH
Confidence 00 000111111111121 147899999999999999999999999942 35999999999
Q ss_pred HHHHHHHHHHHHHh
Q 009012 431 AKDALIQVMTRLRA 444 (546)
Q Consensus 431 v~~A~~~I~~~l~~ 444 (546)
++.|...|..+++.
T Consensus 144 ~~~A~~~I~~li~g 157 (180)
T PRK13763 144 VEIAREAIEMLIEG 157 (180)
T ss_pred HHHHHHHHHHHHcC
Confidence 99999999888854
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=99.37 E-value=1.6e-12 Score=100.72 Aligned_cols=64 Identities=42% Similarity=0.630 Sum_probs=57.3
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 438 (546)
+.+|+||.+.+|+|||++|++|++|+++|||+|++.+... ....+|.|+|+|+++++..|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhh
Confidence 3689999999999999999999999999999999976432 246789999999999999999987
No 16
>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=99.32 E-value=3.9e-12 Score=98.53 Aligned_cols=64 Identities=52% Similarity=0.778 Sum_probs=57.7
Q ss_pred EEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009012 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 141 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (546)
+++|+||.+.+++||||+|++|++|+++|||+|++.+... + ...+|+|+|+|++++|.+|+.+|
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I 64 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLI 64 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhh
Confidence 3799999999999999999999999999999999987543 1 36799999999999999999887
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.25 E-value=6.4e-11 Score=122.40 Aligned_cols=271 Identities=23% Similarity=0.286 Sum_probs=168.7
Q ss_pred CCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHH
Q 009012 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFK 118 (546)
Q Consensus 39 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~ 118 (546)
.++++..++.+|+..+..||||.|.+|+.|+..|++||.+.+.. -.++++.++.|-+.. +++|..++
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~g~e~~~~~~~~p~~----------v~~a~a~~-- 130 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-VGDERVLLISGFPVQ----------VCKAKAAI-- 130 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCCC----------CChHHHHH--
Confidence 36789999999999999999999999999999999999996542 223566666654433 55555543
Q ss_pred HHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCH
Q 009012 119 VHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA 198 (546)
Q Consensus 119 i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~ 198 (546)
++++. ....+...+-+|...++.|+|++|+++++|+..++|+|.+..... ...++...|.+..
T Consensus 131 -~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ngr-----~g~~~~~~i~~qq 193 (608)
T KOG2279|consen 131 -HQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNGR-----LGLSRLIKISGQQ 193 (608)
T ss_pred -HHHHh-----------cCCcccccccchhhhcccccccchhhhcchhcccccccccccccc-----cccccceeccccc
Confidence 33232 345667889999999999999999999999999999999866421 2457888899988
Q ss_pred HHHHHHHHHHHHHHhcCCCC-------cchhhc-ccccC-----CCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCC
Q 009012 199 SVVKKALCQIASRLHDNPSR-------SQHLLA-SAISN-----SHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAG 265 (546)
Q Consensus 199 ~~V~~A~~~I~~~l~~~~~~-------~~~~~~-~~~~~-----~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~ 265 (546)
..+..|..++.+.+.++..- .+.... ....+ ++..++...+...+-.-..++|-.+....-.+|+.-
T Consensus 194 k~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v 273 (608)
T KOG2279|consen 194 KEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAV 273 (608)
T ss_pred chHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCccee
Confidence 88889999998888764211 111000 00001 111111111000000000011100000000001000
Q ss_pred CC-CCCCCCCCCCC---CCCccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCc---eEEEEecCcc
Q 009012 266 DW-SRSLYSAPRDD---LSSKEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDD---CLITVSSKEF 338 (546)
Q Consensus 266 ~~-~~~~~~~~~~~---~~~~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~---rvi~I~G~~~ 338 (546)
.. -...+..|.+. ........+|.+|...+|.|||+.|+.++.+...+++.+.|.-......- .++.+.|+..
T Consensus 274 ~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~v~~~qic~~egkqh 353 (608)
T KOG2279|consen 274 VVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSRVLQLQICVNEGKQH 353 (608)
T ss_pred EEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccccchhhhhhhheecchhH
Confidence 00 00111222221 23344577899999999999999999999999999999988765433221 3455667654
Q ss_pred h
Q 009012 339 F 339 (546)
Q Consensus 339 ~ 339 (546)
.
T Consensus 354 ~ 354 (608)
T KOG2279|consen 354 Y 354 (608)
T ss_pred H
Confidence 3
No 18
>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=99.23 E-value=1.6e-11 Score=94.27 Aligned_cols=61 Identities=21% Similarity=0.323 Sum_probs=54.7
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 439 (546)
.+|.||..++++|||++|++|++|+++|||+|.++... +.++.|+|+|++++|..|+.+|+
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 57999999999999999999999999999999996532 45689999999999999998873
No 19
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.21 E-value=3.5e-11 Score=124.28 Aligned_cols=232 Identities=24% Similarity=0.359 Sum_probs=167.5
Q ss_pred CCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009012 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 136 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (546)
....+.+++.||...+-++|||.|.+|+.|+..|+++|.+..+ +.+ .++...+.|-+.+|.+|...+..++..+
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e-d~g-----~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE-DVG-----DERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc-cCC-----cccchhhccCCCCCChHHHHHHHHHhcC
Confidence 3466789999999999999999999999999999999988654 332 3666667778999999999999988664
Q ss_pred CCCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcc
Q 009012 216 PSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANI 295 (546)
Q Consensus 216 ~~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~ 295 (546)
+ .+.+.+.+|...+
T Consensus 138 ~------------------------------------------------------------------pvk~~lsvpqr~~ 151 (608)
T KOG2279|consen 138 T------------------------------------------------------------------PVSEQLSVPQRSV 151 (608)
T ss_pred C------------------------------------------------------------------cccccccchhhhc
Confidence 1 3456678899999
Q ss_pred cccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhh--------chHHHHHHHHh----c---Cc---c
Q 009012 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDT--------LSATIEAVVRL----Q---PR---C 357 (546)
Q Consensus 296 g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~--------~~~~~~a~~~~----~---~~---~ 357 (546)
+.|+|++|++++.|+..++|+|.++.+......+++.|.+....+.. +..-.+.+.+. + ++ .
T Consensus 152 ~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~ 231 (608)
T KOG2279|consen 152 GRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPI 231 (608)
T ss_pred ccccccchhhhcchhcccccccccccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCc
Confidence 99999999999999999999999998866666677777765332210 00000000000 0 00 0
Q ss_pred c---cc------------------ccc--------c-----------------------cCCcceeEEEEEcCCcceeEE
Q 009012 358 S---EK------------------IER--------D-----------------------SGLISFTTRLLVPTSRIGCLI 385 (546)
Q Consensus 358 ~---~~------------------~~~--------~-----------------------~~~~~~~~~l~VP~~~vG~II 385 (546)
+ +. ... + .........|.||...+|.||
T Consensus 232 n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~li 311 (608)
T KOG2279|consen 232 NVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLI 311 (608)
T ss_pred cccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchh
Confidence 0 00 000 0 011234467999999999999
Q ss_pred cCCChhHHHHHHhcCceEEEecCCCCCCCCCC-CCceEEEEcCHHHHHHHHHHHHHHH
Q 009012 386 GKGGSIITEMRRLTKANIRILPKENLPKIASE-DDEMVQISGDLDLAKDALIQVMTRL 442 (546)
Q Consensus 386 GkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~-~~r~v~I~G~~~~v~~A~~~I~~~l 442 (546)
|+.|+.|+.+...|++.+.|.. .|..... .-.++.+.|+..-+..|+.|+..+.
T Consensus 312 g~~gey~s~yssasn~~~hi~t---~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 312 GHAGEYLSVYSSASNHPNHIWT---QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred hhhhhhhhhhhhccCccceEEe---ccccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 9999999999999999988854 3441111 1145789999999999999997443
No 20
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.19 E-value=7.3e-11 Score=89.94 Aligned_cols=58 Identities=26% Similarity=0.342 Sum_probs=52.6
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHH
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQV 438 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I 438 (546)
.+..|.||.+++|+|||++|++|++|+++|||+|.|.. ++.|.|.|+ +++++.|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 45779999999999999999999999999999999942 358999998 99999999887
No 21
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.18 E-value=4.7e-11 Score=133.67 Aligned_cols=304 Identities=21% Similarity=0.273 Sum_probs=195.9
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHH-
Q 009012 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHD- 121 (546)
Q Consensus 43 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~- 121 (546)
+..++.+....+.+|||++|.+++.++.++.+.|+|++..... ....|.+...++.. ...-.+.++.++..
T Consensus 201 ~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~--~~~~i~~~~~~~~~------~~~~i~~~~~~le~~ 272 (753)
T KOG2208|consen 201 VFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSS--PSNKIDGRLNSSSS------INVEIQEALTRLESE 272 (753)
T ss_pred EEEEeeccccchhhhccccccccccccccceeEEEcccccccc--hhhhhcccccccee------hhhhhHHHHHHhcCh
Confidence 6678999999999999999999999999999999997652222 12333333222110 00001111111100
Q ss_pred ----------------------------HHHHh-hhcCC-C-----------C---------------CCCCCceEEEEE
Q 009012 122 ----------------------------RVIAE-ELRGD-E-----------D---------------SDGGHQVTAKLL 145 (546)
Q Consensus 122 ----------------------------~i~~~-~~~~~-~-----------~---------------~~~~~~~~~~ll 145 (546)
..... .+..+ + + .-....+.+.+-
T Consensus 273 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~ 352 (753)
T KOG2208|consen 273 FDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKRE 352 (753)
T ss_pred hhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEe
Confidence 00000 00000 0 0 012233677888
Q ss_pred eeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCCcchhhcc
Q 009012 146 VPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSRSQHLLAS 225 (546)
Q Consensus 146 Vp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~ 225 (546)
+....+..|+||+|.+|.+|++++.+.|.+... .+.+..+.++|....+.+|...|...+.+.+.
T Consensus 353 i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n-------- 417 (753)
T KOG2208|consen 353 IFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN-------- 417 (753)
T ss_pred ecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc--------
Confidence 889999999999999999999999999998762 25678899999999999999999988876311
Q ss_pred cccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCcccccccCCchh
Q 009012 226 AISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGVIGKGGAI 305 (546)
Q Consensus 226 ~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~iIGk~G~~ 305 (546)
......+.+|...+..|||.+|..
T Consensus 418 --------------------------------------------------------~~~~~~~~iP~k~~~~iig~~g~~ 441 (753)
T KOG2208|consen 418 --------------------------------------------------------SIVKEEVQIPTKSHKRIIGTKGAL 441 (753)
T ss_pred --------------------------------------------------------ccccceeecCccchhhhhcccccc
Confidence 023456899999999999999999
Q ss_pred HHHHHhhhC-CeEEecCCCCCCCceEEEEecCcc-hhhhchHHHHHHHHhcCccccccccccCCcceeEEEEEcCCccee
Q 009012 306 INQIRQESG-AAIKVDSSSTEGDDCLITVSSKEF-FEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRLLVPTSRIGC 383 (546)
Q Consensus 306 Ik~i~~~sg-a~I~i~~~~~~~~~rvi~I~G~~~-~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l~VP~~~vG~ 383 (546)
|+.|..+++ ..|.+.......+ ..++.+... ++. ....+..+.. ...........+...+.|..+.+.
T Consensus 442 i~~I~~k~~~v~i~f~~~~~~~~--~~~~~~~~~dv~~----~~~~~~~~~~----~a~~~~~~~~~~~d~~~~~~~~~~ 511 (753)
T KOG2208|consen 442 INYIMGKHGGVHIKFQNNNNSSD--MVTIRGISKDVEK----SVSLLKALKA----DAKNLKFRDVVTKDKLLPVKYIGK 511 (753)
T ss_pred HHHHHhhcCcEEEecCCCCcccc--cceEeccccccch----hHHHHHhhhh----hhhcchhhhhhhccccchHHhhcc
Confidence 999999998 7777776543322 233333211 111 1111111100 000001112356677888888888
Q ss_pred EEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009012 384 LIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 384 IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 445 (546)
.+|+.|..+...++.....+.. ..++..++|.|..+.|.+|.+++..++...
T Consensus 512 ~~g~~~~i~d~~~~~~i~~~~~----------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 512 EIGKNGTIRDSLGDKSIFPPNE----------DEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred cccCceeeeccCCceeeccccc----------ccccceeeecccccchhhhHHHHHhcchhh
Confidence 8888776665555544433322 345678999999999999999887777665
No 22
>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=99.17 E-value=1.8e-11 Score=93.24 Aligned_cols=60 Identities=35% Similarity=0.511 Sum_probs=53.9
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 438 (546)
|.+|.||.+++|+|||++|++|++|+++|||+|.++.+ + ....|+|.|++++|+.|+.+|
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 67899999999999999999999999999999999643 1 345899999999999999886
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=99.13 E-value=2.2e-10 Score=88.29 Aligned_cols=62 Identities=37% Similarity=0.599 Sum_probs=55.2
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHH
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQV 438 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 438 (546)
.+|.||.+++++|||++|++|++|+++|||+|.|..... ++.++.|+|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence 579999999999999999999999999999999965322 35678999999999999998876
No 24
>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=99.09 E-value=1.5e-10 Score=88.78 Aligned_cols=60 Identities=28% Similarity=0.441 Sum_probs=54.8
Q ss_pred EEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009012 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 142 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (546)
..|.||.+++++|||++|++|++|+++|||+|.|++.. ..++.|+|+|+.++|.+|+.+|
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 67899999999999999999999999999999997642 4578999999999999998876
No 25
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.09 E-value=7.3e-11 Score=89.90 Aligned_cols=60 Identities=40% Similarity=0.613 Sum_probs=54.1
Q ss_pred EEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009012 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 141 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (546)
|.+|+||.+++++|||++|++|++|+++|||+|.|.++ .....|+|+|+.++|.+|+.+|
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 67899999999999999999999999999999999764 1245899999999999999876
No 26
>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=99.09 E-value=4.1e-10 Score=85.80 Aligned_cols=58 Identities=34% Similarity=0.488 Sum_probs=52.6
Q ss_pred eEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcC-HHHHHHHHHHH
Q 009012 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGE-ASVVKKALCQI 208 (546)
Q Consensus 140 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~-~~~V~~A~~~I 208 (546)
.+..|.||.+++++||||+|++|++|+++|||+|.|.+ ++.|.|+|+ .+++.+|+.+|
T Consensus 2 ~~~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg~~I~i~~-----------~g~v~I~G~~~~~v~~A~~~I 60 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETGVKIDIED-----------DGTVYIAASDKEAAEKAKKMI 60 (61)
T ss_pred eEEEEEeChhheeeeECCCchHHHHHHHHHCCEEEeCC-----------CCEEEEEeCCHHHHHHHHHHh
Confidence 46789999999999999999999999999999999854 457999998 99999998876
No 27
>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=99.01 E-value=1.2e-09 Score=84.25 Aligned_cols=62 Identities=40% Similarity=0.657 Sum_probs=55.6
Q ss_pred EEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHH
Q 009012 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 142 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I 208 (546)
.+|.||..++++|||++|++|++|+++|||+|.|..... ...++.|.|.|+.+++..|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~-----~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSGS-----GSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCCCC-----CCCceEEEEEcCHHHHHHHHHHh
Confidence 689999999999999999999999999999999976532 24688999999999999998776
No 28
>PF13014 KH_3: KH domain
Probab=98.94 E-value=1.8e-09 Score=76.24 Aligned_cols=42 Identities=48% Similarity=0.794 Sum_probs=38.9
Q ss_pred ccceEecCCcHHHHHHHHHhCCeEEEcC-CCCCCcceEEEEec
Q 009012 53 KIGSIIGRGGEIVKQLRIDTKSKIRIGE-TVPGSEERVVTVYS 94 (546)
Q Consensus 53 ~vg~IIGk~G~~Ik~I~~~tga~I~i~~-~~~~~~ervv~I~G 94 (546)
+||+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
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 5899999999999999999999999988 56788899999987
No 29
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.86 E-value=4.9e-09 Score=117.68 Aligned_cols=288 Identities=19% Similarity=0.252 Sum_probs=188.1
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHH
Q 009012 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDR 122 (546)
Q Consensus 43 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~ 122 (546)
....+.+-...+..|+||+|.+|.+|++++.|.|.+.+. +..+..+++++...++ ..|.+.+..+...
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~----------~ka~~~v~~~~~e 414 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAND----------EKAVEDVEKIIAE 414 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccch----------hHHHHHHHHHHHh
Confidence 556777888999999999999999999999999999875 5667789999987763 2234443333332
Q ss_pred HHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcC-ceEEEecCCCCCcccCCCCceEEEEcCHHHH
Q 009012 123 VIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG-AQIRILKDEHLPSCALRSDELVQISGEASVV 201 (546)
Q Consensus 123 i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V 201 (546)
+. . ..+...+++|...+.++||.+|..|+.|.++++ ..|++.... +....+++.|....|
T Consensus 415 i~----n--------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~dv 475 (753)
T KOG2208|consen 415 IL----N--------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISKDV 475 (753)
T ss_pred hh----c--------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEecccccc
Confidence 21 1 144577999999999999999999999999999 666554432 334568888888888
Q ss_pred HHHHHHHHHHHhcCCCCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009012 202 KKALCQIASRLHDNPSRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSS 281 (546)
Q Consensus 202 ~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~ 281 (546)
..+..+...+........ | .
T Consensus 476 ~~~~~~~~~~~~~a~~~~-----------------------------------------------~-------------~ 495 (753)
T KOG2208|consen 476 EKSVSLLKALKADAKNLK-----------------------------------------------F-------------R 495 (753)
T ss_pred chhHHHHHhhhhhhhcch-----------------------------------------------h-------------h
Confidence 776665554443211000 0 0
Q ss_pred ccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCcccccc
Q 009012 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI 361 (546)
Q Consensus 282 ~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~ 361 (546)
.........|..+.+..+|+.+..+..+.++. .++..... +...++|.|...... .+.+++..+.+.+..
T Consensus 496 ~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~----i~~~~~~~-~~~~i~i~gk~~~v~---~a~~~L~~~~~~~~~-- 565 (753)
T KOG2208|consen 496 DVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKS----IFPPNEDE-DHEKITIEGKLELVL---EAPAELKALIEALIK-- 565 (753)
T ss_pred hhhhccccchHHhhcccccCceeeeccCCcee----eccccccc-ccceeeecccccchh---hhHHHHHhcchhhhh--
Confidence 01233455666666677777666555555444 44443222 567888888753222 122222222222221
Q ss_pred ccccCCcceeEEEEEcCCcc-eeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 009012 362 ERDSGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (546)
Q Consensus 362 ~~~~~~~~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 440 (546)
.....+.+|..++ -+|++++....+..+...|+.+..++.. .+.+.++|.|..+.++.|...+.+
T Consensus 566 -------~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~~-------~~~~e~~i~g~~~~v~aa~~~~~~ 631 (753)
T KOG2208|consen 566 -------ATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRSP-------TSSDEVSIKGAKDEVKAAKGRLEE 631 (753)
T ss_pred -------hhhhhccCcchheeeeeeccccccccceeecCcccccCCCCC-------CchhhhccchhHHHHHHhhccchh
Confidence 1233455555555 7788888888888888888888775432 334479999999999999887776
Q ss_pred HHHhc
Q 009012 441 RLRAN 445 (546)
Q Consensus 441 ~l~~~ 445 (546)
.+...
T Consensus 632 i~~~~ 636 (753)
T KOG2208|consen 632 IVEYL 636 (753)
T ss_pred hhhhc
Confidence 66543
No 30
>PF13014 KH_3: KH domain
Probab=98.86 E-value=4.5e-09 Score=74.18 Aligned_cols=43 Identities=49% Similarity=0.797 Sum_probs=37.2
Q ss_pred cceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc
Q 009012 380 RIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG 426 (546)
Q Consensus 380 ~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G 426 (546)
+||+|||++|++|++|+++|||+|+|++ +..| .++++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~~---~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENEP---GSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccCC---CCCceEEEEEC
Confidence 5899999999999999999999999977 2222 57789999997
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.84 E-value=1.8e-08 Score=78.14 Aligned_cols=66 Identities=29% Similarity=0.519 Sum_probs=58.6
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRL 442 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 442 (546)
.+.++.||..++++|||++|++|++|++.|+++|.+.... .....|+|.|+.+++..|+.+|.+.+
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 6788999999999999999999999999999999995421 24678999999999999999998876
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.80 E-value=9.9e-08 Score=87.88 Aligned_cols=148 Identities=25% Similarity=0.306 Sum_probs=101.9
Q ss_pred CceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHH
Q 009012 41 EDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVH 120 (546)
Q Consensus 41 ~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~ 120 (546)
......+.||...++.+||+.|++.+.|++.++++|.+ +..+..|.|........ .-++.+..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~i-----D~~~~~V~i~~~~~t~D------------p~~~~ka~ 68 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRI-----DSKTGSVTIRTTRKTED------------PLALLKAR 68 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEE-----ECCCCeEEEEecCCCCC------------hHHHHHHH
Confidence 34457799999999999999999999999999999999 55677899987632111 11222222
Q ss_pred HHHHHh--hhcCCCCC-CCCCceEEEE-----Eee--C----CceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009012 121 DRVIAE--ELRGDEDS-DGGHQVTAKL-----LVP--S----DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 121 ~~i~~~--~~~~~~~~-~~~~~~~~~l-----lVp--~----~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+.+- .+..+... -....+.+.+ ++- . ...|+|||++|.|-+.|++-|+|.|.|.
T Consensus 69 d~VkAIgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~---------- 138 (194)
T COG1094 69 DVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVY---------- 138 (194)
T ss_pred HHHHHHhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEe----------
Confidence 222211 11110000 0001222221 111 1 2469999999999999999999999985
Q ss_pred CCCceEEEEcCHHHHHHHHHHHHHHHhcCCC
Q 009012 187 RSDELVQISGEASVVKKALCQIASRLHDNPS 217 (546)
Q Consensus 187 ~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~ 217 (546)
+..|.|-|..++|..|..+|..+|...++
T Consensus 139 --g~tVaiiG~~~~v~iAr~AVemli~G~~h 167 (194)
T COG1094 139 --GKTVAIIGGFEQVEIAREAVEMLINGAPH 167 (194)
T ss_pred --CcEEEEecChhhhHHHHHHHHHHHcCCCc
Confidence 44799999999999999999999977543
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.73 E-value=6.4e-08 Score=74.98 Aligned_cols=67 Identities=39% Similarity=0.655 Sum_probs=59.4
Q ss_pred ceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHH
Q 009012 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRL 212 (546)
Q Consensus 139 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l 212 (546)
.++.++.||...++.|||++|.+|++|++.|+++|.+.... .....+.|.|..+++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~-------~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDG-------SEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCC-------CCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 35789999999999999999999999999999999996532 14688999999999999999998876
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.67 E-value=1.4e-07 Score=86.95 Aligned_cols=145 Identities=24% Similarity=0.321 Sum_probs=97.1
Q ss_pred cEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhch-----HHHHHHHHhcCc-
Q 009012 283 EFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLS-----ATIEAVVRLQPR- 356 (546)
Q Consensus 283 ~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~-----~~~~a~~~~~~~- 356 (546)
.....+.||.+.++.+||+.|+..+.|.+.++++|.++.. +..|+|...+...|++. ..+.|+-+-++.
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 KSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTEDPLALLKARDVVKAIGRGFPPE 81 (194)
T ss_pred cceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCChHHHHHHHHHHHHHhcCCCHH
Confidence 3467799999999999999999999999999999999863 45677776543223221 122222111110
Q ss_pred cccc-cccccCCcceeEE-EEE-c----CCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 009012 357 CSEK-IERDSGLISFTTR-LLV-P----TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (546)
Q Consensus 357 ~~~~-~~~~~~~~~~~~~-l~V-P----~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~ 429 (546)
-.-. ++++.-...+... +.- + ....|.|||++|.+-+-|++.|+|+|.|.. .+|.|.|+++
T Consensus 82 ~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVaiiG~~~ 149 (194)
T COG1094 82 KALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVAIIGGFE 149 (194)
T ss_pred HHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEEEecChh
Confidence 0000 0010000000000 011 1 234699999999999999999999999963 3899999999
Q ss_pred HHHHHHHHHHHHHHh
Q 009012 430 LAKDALIQVMTRLRA 444 (546)
Q Consensus 430 ~v~~A~~~I~~~l~~ 444 (546)
+|+.|...|..+|..
T Consensus 150 ~v~iAr~AVemli~G 164 (194)
T COG1094 150 QVEIAREAVEMLING 164 (194)
T ss_pred hhHHHHHHHHHHHcC
Confidence 999999999888865
No 35
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.40 E-value=1.1e-06 Score=76.20 Aligned_cols=67 Identities=22% Similarity=0.351 Sum_probs=51.8
Q ss_pred CCcceeEEcCCChhHHHHHHhcCceEEEecCCCC-----------CCCCC-CCCceEEEEcC---HHHHHHHHHHHHHHH
Q 009012 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENL-----------PKIAS-EDDEMVQISGD---LDLAKDALIQVMTRL 442 (546)
Q Consensus 378 ~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~-----------P~~~~-~~~r~v~I~G~---~~~v~~A~~~I~~~l 442 (546)
.+++|.|||++|.+||+|+++|||+|.|..+... |.... ++.-.|.|+++ .+++..|+.+|..+|
T Consensus 14 ~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll 93 (120)
T cd02395 14 YNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELL 93 (120)
T ss_pred CCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHh
Confidence 4688999999999999999999999999765311 11111 12246999995 599999999999888
Q ss_pred Hh
Q 009012 443 RA 444 (546)
Q Consensus 443 ~~ 444 (546)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 74
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=98.31 E-value=2.1e-06 Score=74.42 Aligned_cols=67 Identities=25% Similarity=0.391 Sum_probs=51.7
Q ss_pred CceeEEeccCchHHHHHHhhcCceEEEecCCCCCc------------ccCCCCceEEEEcCH---HHHHHHHHHHHHHHh
Q 009012 149 DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPS------------CALRSDELVQISGEA---SVVKKALCQIASRLH 213 (546)
Q Consensus 149 ~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~------------~~~~~dr~v~I~G~~---~~V~~A~~~I~~~l~ 213 (546)
+.+|.|||++|.+||+|+++|||+|.|..+..... ......-.|.|++.. +++.+|+.+|..++.
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 57899999999999999999999999976521100 001223578899964 999999999999987
Q ss_pred cC
Q 009012 214 DN 215 (546)
Q Consensus 214 ~~ 215 (546)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 54
No 37
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.24 E-value=8.6e-07 Score=86.08 Aligned_cols=143 Identities=17% Similarity=0.237 Sum_probs=101.0
Q ss_pred ccEEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCcc----
Q 009012 282 KEFSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRC---- 357 (546)
Q Consensus 282 ~~~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~---- 357 (546)
..++..+.||..+++.|.|++|++||.|+.+|..+|+-+... .+.++.++|.....+.+...++++..-+..+
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~edv~~aRrei~saaeH~~l~~~s~ 100 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRHEDVRRARREIPSAAEHFGLIRASR 100 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCchhHHHHhhcCccccceeeeeeecc
Confidence 457888999999999999999999999999999999887542 4589999996432222221222211111000
Q ss_pred --ccccccccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHH-HHHH
Q 009012 358 --SEKIERDSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDL-AKDA 434 (546)
Q Consensus 358 --~~~~~~~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~-v~~A 434 (546)
...........+.+..+.||...+|.|.|..|.+|+.|++.+...|.-+-++ .+-++-++|-+.+ +++|
T Consensus 101 s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~nC~kra 172 (394)
T KOG2113|consen 101 SFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPKNCVKRA 172 (394)
T ss_pred cccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCcchhhhc
Confidence 0000111123467888999999999999999999999999999999876543 3458899998877 4444
Q ss_pred H
Q 009012 435 L 435 (546)
Q Consensus 435 ~ 435 (546)
.
T Consensus 173 ~ 173 (394)
T KOG2113|consen 173 R 173 (394)
T ss_pred c
Confidence 4
No 38
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=98.15 E-value=9.6e-06 Score=89.65 Aligned_cols=96 Identities=25% Similarity=0.327 Sum_probs=78.5
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009012 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+..|.+++..|++.+.+..... .+.....+....|.||.+.++.|||++|.+||.|+++|||+|.|..
T Consensus 546 ~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------- 615 (719)
T TIGR02696 546 SALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec---------
Confidence 467788889989888665544433 3344556678899999999999999999999999999999999953
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 187 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
+..|.|.+ +.+++.+|+.+|..++..
T Consensus 616 --~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 --DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred --CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 56788888 578999999999998864
No 39
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.09 E-value=6.1e-06 Score=73.73 Aligned_cols=102 Identities=18% Similarity=0.262 Sum_probs=69.5
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHH
Q 009012 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 44 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i 123 (546)
.+.++|+...+|..||++|++|+.|++..|-+|.|- .-+-. +++-+..++.-.
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVv-----------e~s~d----------------~~~fI~n~l~Pa 85 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELV-----------EYSDD----------------PEEFIKNIFAPA 85 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEE-----------EcCCC----------------HHHHHHHHcCCC
Confidence 357888999999999999999999999999888752 21111 122221111110
Q ss_pred HHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEE
Q 009012 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (546)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 175 (546)
.-..+.- ........+.+.|+....+.+|||+|++|+.++.-++-.+.|
T Consensus 86 ~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 86 AVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 0000000 011233567788999999999999999999999999998876
No 40
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.94 E-value=1.3e-05 Score=77.95 Aligned_cols=142 Identities=24% Similarity=0.359 Sum_probs=102.9
Q ss_pred CCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009012 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (546)
Q Consensus 137 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 216 (546)
...++..+.||..+++.|.|++|.+||.|+.+|...|.-+..++ +-+..++|..+.|+.|...|...-+..-
T Consensus 23 p~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~e--------ePiF~vTg~~edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 23 GQNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGE--------EPIFPVTGRHEDVRRARREIPSAAEHFG 94 (394)
T ss_pred CCccceeeecCcccceeecccCccccchhhhhhcceeccCCCCC--------CCcceeccCchhHHHHhhcCccccceee
Confidence 37788999999999999999999999999999999998765543 3468899999999999988765332210
Q ss_pred CCcchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCccc
Q 009012 217 SRSQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIG 296 (546)
Q Consensus 217 ~~~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g 296 (546)
+.-.. ..|.. +. + + + ..+.+....+.+|...++
T Consensus 95 ------l~~~s-~s~Sg---------g~------~-------------~------~------s~s~qt~sy~svP~rvvg 127 (394)
T KOG2113|consen 95 ------LIRAS-RSFSG---------GT------N-------------G------A------SASGQTTSYVSVPLRVVG 127 (394)
T ss_pred ------eeeec-ccccC---------CC------c-------------c------c------cccCCCceeeeccceeee
Confidence 00000 00000 00 0 0 0 012345677889999999
Q ss_pred ccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecC
Q 009012 297 GVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSK 336 (546)
Q Consensus 297 ~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~ 336 (546)
.|.|..|.+|+.|++.+...|.-+-.. .+.++.++|.
T Consensus 128 lvv~~~~~ti~~iqq~tnt~I~T~v~~---~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 128 LVVGPKGATIKRIQQFTNTYIATPVRC---GEPVFCVTGA 164 (394)
T ss_pred eccccccCccchheecccceEeeeccC---CCceEEEecC
Confidence 999999999999999999888776543 4568888874
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.93 E-value=4.7e-05 Score=68.02 Aligned_cols=103 Identities=20% Similarity=0.268 Sum_probs=71.3
Q ss_pred EEEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCcccccccc
Q 009012 284 FSLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIER 363 (546)
Q Consensus 284 ~~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~ 363 (546)
..+.++|+...+|..||++|++|+.|++..|-+|.+-.-+.+ . ..-+..++.. .-.....-
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-------------~----~~fI~n~l~P--a~V~~v~I 92 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-------------P----EEFIKNIFAP--AAVRSVTI 92 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-------------H----HHHHHHHcCC--CEEEEEEE
Confidence 377889999999999999999999999988988877643211 0 1122222211 11111100
Q ss_pred ccCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEE
Q 009012 364 DSGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 364 ~~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i 405 (546)
..........+.|+.+..|..|||+|++|+.+++.++-.+.|
T Consensus 93 ~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 93 KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 001112456688999999999999999999999999988877
No 42
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.90 E-value=8.6e-05 Score=76.87 Aligned_cols=77 Identities=25% Similarity=0.385 Sum_probs=59.4
Q ss_pred ceeEEEEEc------CCcceeEEcCCChhHHHHHHhcCceEEEecCCC----------CCCCCCCCCc-eEEEEcC-HHH
Q 009012 369 SFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKEN----------LPKIASEDDE-MVQISGD-LDL 430 (546)
Q Consensus 369 ~~~~~l~VP------~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~----------~P~~~~~~~r-~v~I~G~-~~~ 430 (546)
.++.+|.|| .++||+|||..|.+.|+|+++|||+|.|-.+.. +.....+.+. -+.|+.+ .|.
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 567788888 468999999999999999999999999977321 1111123333 3888885 789
Q ss_pred HHHHHHHHHHHHHhc
Q 009012 431 AKDALIQVMTRLRAN 445 (546)
Q Consensus 431 v~~A~~~I~~~l~~~ 445 (546)
|++|+.+|..+|.+.
T Consensus 217 i~~Ai~vienli~~a 231 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999988864
No 43
>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=97.78 E-value=5.1e-05 Score=84.05 Aligned_cols=65 Identities=28% Similarity=0.340 Sum_probs=57.9
Q ss_pred ceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009012 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (546)
....+|.||.+++|.|||+||.+||+|.++|||+|.|. ++..|.|.+ +.+++++|+.+|...+..
T Consensus 577 P~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~-----------d~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 577 PRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIE-----------DDGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEe-----------cCcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 46678999999999999999999999999999999994 246888888 689999999999888874
No 44
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.68 E-value=0.00034 Score=72.52 Aligned_cols=77 Identities=23% Similarity=0.368 Sum_probs=58.0
Q ss_pred CceEEEEEeeC------CceeEEeccCchHHHHHHhhcCceEEEecCCCC----------Ccc-cCCCCceEEEEcC-HH
Q 009012 138 HQVTAKLLVPS------DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHL----------PSC-ALRSDELVQISGE-AS 199 (546)
Q Consensus 138 ~~~~~~llVp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~----------p~~-~~~~dr~v~I~G~-~~ 199 (546)
..++.+|.||- +.||+|||..|.|.|+|+.+|||+|.|..+..+ ... ....+=.|.|+.+ -|
T Consensus 136 ~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~e 215 (554)
T KOG0119|consen 136 AKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQE 215 (554)
T ss_pred cccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHH
Confidence 36788888884 578999999999999999999999999752211 100 0122235778885 58
Q ss_pred HHHHHHHHHHHHHhc
Q 009012 200 VVKKALCQIASRLHD 214 (546)
Q Consensus 200 ~V~~A~~~I~~~l~~ 214 (546)
.|++|+..|..+|.+
T Consensus 216 ki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 216 KIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHh
Confidence 899999999998876
No 45
>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=97.66 E-value=0.00011 Score=82.61 Aligned_cols=96 Identities=21% Similarity=0.290 Sum_probs=73.0
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009012 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+..|.+++.+|++.+.+.......+.....+....+.||.+.++.|||++|.+||.|+++|||+|.|..
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------- 588 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------- 588 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec---------
Confidence 44566777777887765543333222234445677889999999999999999999999999999999954
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHh
Q 009012 187 RSDELVQISG-EASVVKKALCQIASRLH 213 (546)
Q Consensus 187 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~ 213 (546)
+..|.|.+ ..+.+.+|...|..+..
T Consensus 589 --dG~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 589 --DGTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred --CeEEEEEECcHHHHHHHHHHHHhhhc
Confidence 45677776 57888999998888764
No 46
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.64 E-value=5.8e-05 Score=76.66 Aligned_cols=64 Identities=28% Similarity=0.459 Sum_probs=54.9
Q ss_pred CCCCCCcccCCCceEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCC
Q 009012 30 GDDRDQFIIGPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSAS 96 (546)
Q Consensus 30 ~~~~~~~~~~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~ 96 (546)
.+.++.-+.+.+++.+++.|-+++||.|||++|++|++|+..|+++|+|.+. ..+-.|+|.|..
T Consensus 34 ~~~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~ 97 (629)
T KOG0336|consen 34 RDSRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGIN 97 (629)
T ss_pred CCCCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechH
Confidence 3556666778899999999999999999999999999999999999999654 345688999974
No 47
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.57 E-value=0.00014 Score=82.48 Aligned_cols=97 Identities=21% Similarity=0.242 Sum_probs=76.5
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCce-EEEecCCCCCccc
Q 009012 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQ-IRILKDEHLPSCA 185 (546)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~ 185 (546)
+.+..|.+++..|++.+.+.......+.....+....|.||.+.++.|||.+|.+||.|.++||++ |.+..
T Consensus 652 eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d-------- 723 (891)
T PLN00207 652 RALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD-------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------
Confidence 466778888888887665544333233344566788999999999999999999999999999999 87743
Q ss_pred CCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 186 LRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 186 ~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
+-.|.|.+ +.+.+.+|+..|..++.+
T Consensus 724 ---dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 ---DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ---CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 55688888 678999999999988754
No 48
>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=97.53 E-value=0.00029 Score=62.84 Aligned_cols=102 Identities=23% Similarity=0.308 Sum_probs=70.7
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccc
Q 009012 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 285 ~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
.+-|+|....+|..||++|++|+.|++..|-+|.+-.-+.+ . ..-+..+ +.|.-...+.-.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-------------~----~~fI~N~--l~PA~V~~V~i~ 94 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-------------L----EEFVANK--LAPAEVKNVTVS 94 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-------------H----HHHHHHc--CCCceEEEEEEE
Confidence 67789999999999999999999998888888877543211 0 1111111 112111111110
Q ss_pred cCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEE
Q 009012 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i 405 (546)
..+......+.||.+..+..|||+|.+|+-..+.++-++.|
T Consensus 95 ~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 95 EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 01123557788999999999999999999999999988877
No 49
>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=97.52 E-value=0.00011 Score=65.39 Aligned_cols=103 Identities=22% Similarity=0.276 Sum_probs=68.9
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHH
Q 009012 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 44 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i 123 (546)
.+-++|....+|..||++|++|+.|++..|-+|.|- .-+..+++ - +.+.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVV-----------eys~D~~~----------------f---I~N~l 83 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELI-----------EYSENLEE----------------F---VANKL 83 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEE-----------EcCCCHHH----------------H---HHHcC
Confidence 567889999999999999999999998888888752 22221111 0 10000
Q ss_pred HHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEe
Q 009012 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRIL 176 (546)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 176 (546)
.-..+..-............+.||.++.+..|||+|++|+...+-++-++.|.
T Consensus 84 ~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 84 APAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 00000000000112335677899999999999999999999999999888763
No 50
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.48 E-value=0.00017 Score=78.30 Aligned_cols=114 Identities=23% Similarity=0.249 Sum_probs=84.6
Q ss_pred EEEecCCcccccccc-----------CcccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccC
Q 009012 90 VTVYSASDETNAFED-----------GDKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKG 158 (546)
Q Consensus 90 v~I~G~~e~~~~~e~-----------~~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~ 158 (546)
+.|.|+.+.+.+++. ....+..|.+|..+++..+.+.......+.....+....+.|+.+.+..+||++
T Consensus 491 FKVAGT~~GiTAlQMDiKi~Git~eim~~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~g 570 (692)
T COG1185 491 FKVAGTDDGITALQMDIKIKGITKEIMKKALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPG 570 (692)
T ss_pred eEEecCCCcceeeeeeeeecCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCc
Confidence 555666555544332 124567788888888876654433322233344556688899999999999999
Q ss_pred chHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCH-HHHHHHHHHHHHHHhc
Q 009012 159 GQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA-SVVKKALCQIASRLHD 214 (546)
Q Consensus 159 G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~-~~V~~A~~~I~~~l~~ 214 (546)
|.+|++|.++|||+|+|.. +..|.|.++. +.+.+|+..|..+.++
T Consensus 571 Gk~I~~I~eetg~~Idied-----------dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 571 GKTIKAITEETGVKIDIED-----------DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred ccchhhhhhhhCcEEEecC-----------CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 9999999999999999952 5679999876 7889999999998866
No 51
>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=97.27 E-value=0.00036 Score=78.59 Aligned_cols=65 Identities=26% Similarity=0.326 Sum_probs=55.3
Q ss_pred ceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009012 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (546)
....++.||.+.++.|||+||.+||+|.++|||+|.|.. +..|.|.+ +.+.+++|..+|......
T Consensus 550 p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 550 PRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 466789999999999999999999999999999999942 34677776 678899999988877654
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.12 E-value=0.00089 Score=62.75 Aligned_cols=104 Identities=29% Similarity=0.328 Sum_probs=68.4
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHH
Q 009012 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRV 123 (546)
Q Consensus 44 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i 123 (546)
++-+.+-.+.+|..||++|++|+.|.++.|=+|.|-+- +-.+.+ -+.+|+. -.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~-----------s~d~~~------------fI~nal~----Pa 129 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW-----------SEDPAE------------FIKNALA----PA 129 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEe-----------CCCHHH------------HHHHhcC----cc
Confidence 45566667788999999999999999999977765221 111110 0111111 00
Q ss_pred HHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 124 IAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
.-..+.-. ..... ...+.||.++.+.+|||+|.+++-+.+-||-++.|...
T Consensus 130 ~v~~V~~~---~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 130 EVLSVNIK---EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred eEeEEEEE---eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 00000000 11112 68889999999999999999999999999999999653
No 53
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.96 E-value=0.0033 Score=58.94 Aligned_cols=103 Identities=23% Similarity=0.315 Sum_probs=68.9
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccc
Q 009012 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 285 ~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
...+.+-.+.+|..||++|.+|+.|.++.|-+|.|-.-..+ . ..-+..++. |.-...+.-.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-------------~----~~fI~nal~--Pa~v~~V~~~ 137 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-------------P----AEFIKNALA--PAEVLSVNIK 137 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-------------H----HHHHHHhcC--cceEeEEEEE
Confidence 34455567788999999999999999999976666432211 0 001111111 1111111111
Q ss_pred cCCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEec
Q 009012 365 SGLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~ 407 (546)
..+.. ...+.||.+..+.+|||+|.+++-+.+.||-+|.|..
T Consensus 138 ~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 138 EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 00112 6788899999999999999999999999999999953
No 54
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.86 E-value=0.0015 Score=71.12 Aligned_cols=66 Identities=26% Similarity=0.286 Sum_probs=56.9
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCH-HHHHHHHHHHHHHHHhcc
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDL-DLAKDALIQVMTRLRANL 446 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~~ 446 (546)
-..++.|+.+.+..|||++|.+|++|.++|||+|.|. ++-+|.|.++. +.+..|+..|...+++..
T Consensus 552 ri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-----------ddGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 552 RIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-----------DDGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred ceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-----------CCCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 4578999999999999999999999999999999994 23478888865 888999999988887653
No 55
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.86 E-value=0.0012 Score=74.69 Aligned_cols=97 Identities=22% Similarity=0.319 Sum_probs=72.1
Q ss_pred ccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccC
Q 009012 107 KFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCAL 186 (546)
Q Consensus 107 ~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 186 (546)
+.+..|.+++.+|++.+.+..-..-.+.....+....+.||.+.++.+||++|.+||+|.++||++|.+..
T Consensus 521 ~al~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------- 591 (693)
T PRK11824 521 EALEQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------- 591 (693)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC---------
Confidence 45667888888888776544322222222334455677789999999999999999999999999988732
Q ss_pred CCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 187 RSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 187 ~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
+-.|.|.+ ..+.+.+|+..|..+..+
T Consensus 592 --~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 --DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred --CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 55688888 578889999998887743
No 56
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.83 E-value=0.0021 Score=65.70 Aligned_cols=67 Identities=24% Similarity=0.324 Sum_probs=54.0
Q ss_pred ceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 009012 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 443 (546)
.+...|.|-+.+||.|||++|++|+.|+..|.++|+|..- +.+-.|+|-|...--.+|...|...+.
T Consensus 46 e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 46 EFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred CCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhh
Confidence 3566688899999999999999999999999999999652 335689999998777777666644443
No 57
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.81 E-value=0.0011 Score=75.41 Aligned_cols=65 Identities=20% Similarity=0.303 Sum_probs=56.3
Q ss_pred ceeEEEEEcCCcceeEEcCCChhHHHHHHhcCce-EEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009012 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKAN-IRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~-I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (546)
.....|.||.++++.|||.||.+||+|.++||+. |.|. ++-.|.|.+ +.+.+++|+.+|...+.+
T Consensus 684 P~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 684 PLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 4678899999999999999999999999999999 8873 245788888 689999999999888764
No 58
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.77 E-value=0.006 Score=59.14 Aligned_cols=75 Identities=20% Similarity=0.356 Sum_probs=53.1
Q ss_pred cceeEEEEEcC------CcceeEEcCCChhHHHHHHhcCceEEEecCCCC------------CCCCCCCC---ceEEEEc
Q 009012 368 ISFTTRLLVPT------SRIGCLIGKGGSIITEMRRLTKANIRILPKENL------------PKIASEDD---EMVQISG 426 (546)
Q Consensus 368 ~~~~~~l~VP~------~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~------------P~~~~~~~---r~v~I~G 426 (546)
...+.+|+||- ++||+|+|..|.++|+|+++|||+|-|-.+... |.-++-++ -+|+...
T Consensus 90 vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~~ 169 (259)
T KOG1588|consen 90 VKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETEA 169 (259)
T ss_pred eeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEeC
Confidence 45788999994 589999999999999999999999999877521 22222222 2477777
Q ss_pred CHHHHHH----HHHHHHHHH
Q 009012 427 DLDLAKD----ALIQVMTRL 442 (546)
Q Consensus 427 ~~~~v~~----A~~~I~~~l 442 (546)
++..+.. |++.|...|
T Consensus 170 p~~ea~~rl~~AleeI~klL 189 (259)
T KOG1588|consen 170 PPAEAYARLAYALEEIKKLL 189 (259)
T ss_pred CHHHHHHHHHHHHHHHHHhc
Confidence 7765544 455554444
No 59
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.73 E-value=0.0016 Score=63.11 Aligned_cols=39 Identities=33% Similarity=0.569 Sum_probs=34.9
Q ss_pred CCceEEEEEecCC------ccceEecCCcHHHHHHHHHhCCeEEE
Q 009012 40 PEDTVYRYLCPIR------KIGSIIGRGGEIVKQLRIDTKSKIRI 78 (546)
Q Consensus 40 ~~~~~~rilip~~------~vg~IIGk~G~~Ik~I~~~tga~I~i 78 (546)
+-.++.+|+||.+ +||.|+|++|.++|+|+++|+|+|.|
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~I 133 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMI 133 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEE
Confidence 4456789999998 79999999999999999999999865
No 60
>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=96.49 E-value=0.0049 Score=46.79 Aligned_cols=36 Identities=31% Similarity=0.408 Sum_probs=33.7
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhCCeEEE
Q 009012 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRI 78 (546)
Q Consensus 43 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i 78 (546)
..+.+.||.+.+|.+|||+|.+|+.++..++.+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 578999999999999999999999999999988876
No 61
>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=96.36 E-value=0.0059 Score=62.82 Aligned_cols=96 Identities=30% Similarity=0.428 Sum_probs=62.8
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009012 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|+.|+.|.++. |=+|.|-+- +-.++.. +.+||.-. ++..-.+.
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~~f------------i~nal~Pa--~v~~v~i~- 296 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEY-----------SDDPAEF------------IANALSPA--KVISVEVL- 296 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eEEEEEEE-
Confidence 358999999999999999998 777765211 1111000 00110000 00000000
Q ss_pred CCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
. ...-.+.+.||.++.+..|||+|++++-...-||.+|.|...
T Consensus 297 ----~-~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 297 ----D-EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred ----c-CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 0 122468899999999999999999999999999999999764
No 62
>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=96.33 E-value=0.0065 Score=46.15 Aligned_cols=36 Identities=33% Similarity=0.570 Sum_probs=33.6
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEE
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i 405 (546)
....+.||.+..|.+|||+|.+|+.+++.++-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 567899999999999999999999999999988876
No 63
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.30 E-value=0.0046 Score=61.58 Aligned_cols=71 Identities=27% Similarity=0.391 Sum_probs=57.6
Q ss_pred ceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009012 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 139 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (546)
.....++|++...++|||++|.|-+.|+++|+++|.++...+ +.+.++.+.+..++|.+|...|.-+|...
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 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNT------NKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCCC------CcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 456778999999999999999999999999999998876421 23444444557899999999999888664
No 64
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.18 E-value=0.0079 Score=61.94 Aligned_cols=95 Identities=18% Similarity=0.173 Sum_probs=62.6
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009012 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|.+|+.|.++. |=+|.|-.- .-.++ + .+...+.-..+..
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~-----------s~D~~----------------~---fI~Nal~Pa~V~~ 300 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEY-----------SNVPE----------------I---FIARALAPAIISS 300 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHH----------------H---HHHHhCCCceeeE
Confidence 358999999999999999998 777765211 11100 0 0100000000000
Q ss_pred CCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
-. .. ...-.+.+.||.++.+..|||+|++++-...-||.+|.|..-
T Consensus 301 V~-i~-~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 301 VK-IE-EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred EE-Ec-CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 00 00 122368889999999999999999999999999999999764
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.17 E-value=0.0066 Score=60.46 Aligned_cols=71 Identities=27% Similarity=0.405 Sum_probs=57.9
Q ss_pred ceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHhcc
Q 009012 369 SFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRANL 446 (546)
Q Consensus 369 ~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~~~ 446 (546)
.....+.|++...|.|||++|.+.+.|+++|+++|.++.+. ++...|+|+| ..++|..|...|...|.+..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~-------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~r 127 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN-------TNKEEIKIIGISRNCVIQALERIAKLIDSDR 127 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC-------CCcceEEEeehhHHHHHHHHHHHHHHHHhhh
Confidence 35677999999999999999999999999999999997642 2334455555 78999999999988887654
No 66
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=96.16 E-value=0.038 Score=51.34 Aligned_cols=42 Identities=26% Similarity=0.590 Sum_probs=36.9
Q ss_pred cceeEEEEEc------CCcceeEEcCCChhHHHHHHhcCceEEEecCC
Q 009012 368 ISFTTRLLVP------TSRIGCLIGKGGSIITEMRRLTKANIRILPKE 409 (546)
Q Consensus 368 ~~~~~~l~VP------~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~ 409 (546)
..++.++.|| .++||.|||..|.+.|+|++.|+|+|-|-.+.
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~g 193 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSG 193 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEeccc
Confidence 3577788888 57899999999999999999999999997654
No 67
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.15 E-value=0.02 Score=59.00 Aligned_cols=97 Identities=21% Similarity=0.202 Sum_probs=65.7
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccccCCccee
Q 009012 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (546)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (546)
+-+|..||++|.+|+.|.++. |-+|.|-.-+.+. ..-+..++ .|.-...+.-. ...-.
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~-----------------~~fI~Nal--~Pa~V~~V~i~--~~~~~ 309 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVP-----------------EIFIARAL--APAIISSVKIE--EEEKK 309 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhC--CCceeeEEEEc--CCCcE
Confidence 468999999999999999998 7777665432210 00111111 11111111111 11246
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCC
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 410 (546)
..+.||.+..+..|||+|.+++-..+.||.+|.|.+-+.
T Consensus 310 ~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 310 AIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred EEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 788999999999999999999999999999999976543
No 68
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.12 E-value=0.0085 Score=62.04 Aligned_cols=96 Identities=24% Similarity=0.304 Sum_probs=63.3
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009012 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|..|+.|.++. |-+|.|-+- .-.++ + .+...+.-..+..
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~-----------s~d~~----------------~---fi~nal~Pa~v~~ 294 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW-----------SEDPA----------------E---FVANALSPAKVVS 294 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEc-----------CCCHH----------------H---HHHHhCCCceEEE
Confidence 458999999999999999998 777775211 11100 0 0100000000000
Q ss_pred CCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
-. ......-.+.+.||.++.+..|||+|++++-...-||.+|.|...
T Consensus 295 v~-i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 295 VE-VDDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EE-EEcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00 000122468899999999999999999999999999999999765
No 69
>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=96.11 E-value=0.019 Score=59.07 Aligned_cols=93 Identities=24% Similarity=0.380 Sum_probs=64.2
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCcccccc--ccccCCcc
Q 009012 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKI--ERDSGLIS 369 (546)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~--~~~~~~~~ 369 (546)
+-+|..||++|.+|+.|.++. |-+|.|-.-+.+. ..-+..++ .|.-...+ ..+ ..
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~-----------------~~fi~nal--~Pa~v~~v~i~~~---~~ 300 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDP-----------------AEFIANAL--SPAKVISVEVLDE---DK 300 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhc--CCceEEEEEEEcC---CC
Confidence 468999999999999999998 7777665432210 00111111 11111111 111 12
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEec
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~ 407 (546)
....+.||.+..+..|||+|.+++-..+.||.+|.|.+
T Consensus 301 ~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 301 HSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred cEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 46789999999999999999999999999999999965
No 70
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.96 E-value=0.022 Score=59.00 Aligned_cols=96 Identities=24% Similarity=0.309 Sum_probs=64.7
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccccCCccee
Q 009012 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (546)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (546)
+-+|..||++|.+|+.|.++. |-+|.|-.-+.+. ..-+..++ .|.-...+.-.. .....
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~-----------------~~fi~nal--~Pa~v~~v~i~~-~~~~~ 304 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDP-----------------AEFVANAL--SPAKVVSVEVDD-EEEKA 304 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhC--CCceEEEEEEEc-CCCcE
Confidence 468999999999999999998 7777665432210 00111111 111111110000 11246
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecC
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (546)
..+.||.+..+..|||+|.+++-..+.||.+|.|.+.
T Consensus 305 ~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 305 ARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 7899999999999999999999999999999999653
No 71
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.87 E-value=0.017 Score=56.59 Aligned_cols=63 Identities=21% Similarity=0.246 Sum_probs=51.6
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcC-HHHHHHHHHHHHHHHHhc
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD-LDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 445 (546)
+.+.||..+++.+||++|.+|+.|.+.|++.|.|- .+-.|.|.++ .+++..|+.+|...-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig-----------~NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVG-----------QNGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEc-----------CCcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 56899999999999999999999999999999983 2357888885 567788877776555443
No 72
>PRK00468 hypothetical protein; Provisional
Probab=95.80 E-value=0.011 Score=46.80 Aligned_cols=34 Identities=24% Similarity=0.501 Sum_probs=30.0
Q ss_pred CCCceEEEEEecCCccceEecCCcHHHHHHHHHh
Q 009012 39 GPEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 39 ~~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~t 72 (546)
..+.+.+++.|..+.+|.||||+|.+|+.||.--
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456789999999999999999999999999654
No 73
>PRK00106 hypothetical protein; Provisional
Probab=95.80 E-value=0.026 Score=61.29 Aligned_cols=65 Identities=25% Similarity=0.334 Sum_probs=50.0
Q ss_pred ceeEEEEEcC-CcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009012 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~-~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~ 443 (546)
..+..|.+|+ ++-|.||||-|.+|+-+...||+.|-|. ++...|+|++ +|---+.|...+..+|.
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid----------dtp~~v~lS~fdpvRReiAr~~le~Li~ 290 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID----------DTPEVVVLSGFDPIRREIARMTLESLIK 290 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc----------CCCCeEEEeCCChHHHHHHHHHHHHHHH
Confidence 4667788998 5669999999999999999999999993 2335899999 77655555555544443
No 74
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.79 E-value=0.0094 Score=62.43 Aligned_cols=95 Identities=29% Similarity=0.323 Sum_probs=61.8
Q ss_pred CccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcC
Q 009012 52 RKIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRG 130 (546)
Q Consensus 52 ~~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~~~ 130 (546)
+-+|..||++|..|+.|.++. |=+|.|-.- +-.++.. +.+||.=. ++..-.+.
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~y-----------s~Dp~~f------------I~NaLsPA--~V~~V~i~- 330 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRW-----------SPDPATY------------IANALSPA--RVDEVRLV- 330 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEc-----------CCCHHHH------------HHHhcCCc--eeeEEEEE-
Confidence 458999999999999999998 777775211 1111000 00100000 00000000
Q ss_pred CCCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEec
Q 009012 131 DEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILK 177 (546)
Q Consensus 131 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 177 (546)
. ...-.+.+.||.++.+..|||+|++|+-...-||.+|.|..
T Consensus 331 ----~-~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 331 ----D-PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred ----c-CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0 11235789999999999999999999999999999999854
No 75
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.71 E-value=0.027 Score=61.44 Aligned_cols=65 Identities=23% Similarity=0.300 Sum_probs=49.3
Q ss_pred ceeEEEEEcC-CcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009012 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~-~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~ 443 (546)
..+..|.+|+ ++-|.||||.|.+|+-+...||+.|-|. + +-..|+|++ +|---+.|...+..+|.
T Consensus 203 ~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~ 269 (514)
T TIGR03319 203 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQ 269 (514)
T ss_pred heeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHH
Confidence 4667788998 5569999999999999999999999993 2 335899999 66555555554444443
No 76
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.70 E-value=0.026 Score=59.22 Aligned_cols=95 Identities=25% Similarity=0.332 Sum_probs=63.6
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccccCCccee
Q 009012 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFT 371 (546)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ 371 (546)
+-+|..||++|.+|+.|.++. |-+|.|-.-+.+. ..-+..++ .|.-...+.-.. .....
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp-----------------~~fI~NaL--sPA~V~~V~i~~-~~~k~ 336 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDP-----------------ATYIANAL--SPARVDEVRLVD-PEGRH 336 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCH-----------------HHHHHHhc--CCceeeEEEEEc-CCCcE
Confidence 468999999999999999998 7777665432210 00111111 111111110000 11235
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEec
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILP 407 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~ 407 (546)
..+.||.++.+..|||+|.+|+-..+.||.+|.|..
T Consensus 337 a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 337 AHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 679999999999999999999999999999999954
No 77
>PRK12704 phosphodiesterase; Provisional
Probab=95.68 E-value=0.027 Score=61.45 Aligned_cols=65 Identities=23% Similarity=0.292 Sum_probs=49.0
Q ss_pred ceeEEEEEcC-CcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHH
Q 009012 369 SFTTRLLVPT-SRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLR 443 (546)
Q Consensus 369 ~~~~~l~VP~-~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~ 443 (546)
..+..|.+|+ ++-|.||||-|.+|+-+...||+.|-|. + +..+|.|+| +|-.-+.|...+...+.
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHh
Confidence 4566788998 5669999999999999999999999993 2 335899999 66554555554444443
No 78
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.63 E-value=0.0075 Score=68.22 Aligned_cols=64 Identities=30% Similarity=0.366 Sum_probs=54.2
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (546)
....+.||.+.++.|||.||.+||+|.++||+.|.+. ++-.|.|.+ +.+.+++|+.+|.....+
T Consensus 554 ~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 554 RIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred hheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 4567888999999999999999999999999988772 245788888 688899999999887754
No 79
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.60 E-value=0.33 Score=46.65 Aligned_cols=131 Identities=17% Similarity=0.166 Sum_probs=87.4
Q ss_pred EEEEEeecCcccccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccc
Q 009012 285 SLRLVCPVANIGGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERD 364 (546)
Q Consensus 285 ~~~v~vp~~~~g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 364 (546)
.+.+.++....-.+...+|..++.|....||+|.+.. +...+.|+|++...+.+...+..++.-
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-----~~~~i~I~g~k~~~~~i~~~i~~~l~~----------- 90 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-----SENRIRITGTKSTAEYIEASINEILSN----------- 90 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-----CCcEEEEEccHHHHHHHHHHHHHHHhh-----------
Confidence 3455556778889999999999999888899999986 356899999864333322233222211
Q ss_pred cCCcceeEEEEEcCCcceeEEc----CCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-----CHHHHHHHH
Q 009012 365 SGLISFTTRLLVPTSRIGCLIG----KGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-----DLDLAKDAL 435 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~vG~IIG----kgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-----~~~~v~~A~ 435 (546)
..+.+|.++.-..-.... .-...+++|++.|++.|..... ...+.|.. +...++.|+
T Consensus 91 ----i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~~~~~~~~~a~ 156 (210)
T PF14611_consen 91 ----IRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASPENEKRADRAK 156 (210)
T ss_pred ----cEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeeccccchHHHHH
Confidence 245556565432111111 1467899999999999998432 23455554 578899999
Q ss_pred HHHHHHHHhc
Q 009012 436 IQVMTRLRAN 445 (546)
Q Consensus 436 ~~I~~~l~~~ 445 (546)
+++...+..+
T Consensus 157 RlL~~a~~~~ 166 (210)
T PF14611_consen 157 RLLLWALDYN 166 (210)
T ss_pred HHHHHhccCC
Confidence 9998888533
No 80
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=95.49 E-value=0.028 Score=59.68 Aligned_cols=114 Identities=18% Similarity=0.214 Sum_probs=78.8
Q ss_pred EEEecCCccccccccC----cccCCHHHHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHH
Q 009012 90 VTVYSASDETNAFEDG----DKFVSPAQDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI 165 (546)
Q Consensus 90 v~I~G~~e~~~~~e~~----~~~v~~a~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I 165 (546)
..|-|+.+.+.++... .+.+.+|.+|-.+|++.+....-..........++...|.|+.+....+||.+|...|+|
T Consensus 543 FKiAGt~dGvTA~gi~l~Iv~eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki 622 (760)
T KOG1067|consen 543 FKIAGTNDGVTALGIPLKIVMEALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKI 622 (760)
T ss_pred eeeccccCcceecCCcHHHHHHHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeE
Confidence 4455666655554221 133455666666777654433333233345567788999999999999999999999999
Q ss_pred HhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhcC
Q 009012 166 RSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHDN 215 (546)
Q Consensus 166 ~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~~ 215 (546)
+.+||+.-.+ ++..+.|-- +..+.++|...|..++..+
T Consensus 623 ~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 623 EVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred eeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 9999955544 245677765 5777899999999888663
No 81
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.39 E-value=0.04 Score=51.18 Aligned_cols=44 Identities=23% Similarity=0.384 Sum_probs=37.0
Q ss_pred CCCCceEEEEEee------CCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 135 DGGHQVTAKLLVP------SDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 135 ~~~~~~~~~llVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
-.....+-++.|| .+.||+|||+.|.|.|+|+..|+|+|-|-..
T Consensus 143 ~rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 143 IRPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cCcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3445567777777 4679999999999999999999999999764
No 82
>PRK02821 hypothetical protein; Provisional
Probab=95.39 E-value=0.017 Score=45.78 Aligned_cols=34 Identities=24% Similarity=0.381 Sum_probs=30.1
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009012 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 40 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tg 73 (546)
.+.+.+.|.|..+.+|.||||+|.+|+.||.--.
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 4557899999999999999999999999997654
No 83
>PRK02821 hypothetical protein; Provisional
Probab=95.34 E-value=0.032 Score=44.30 Aligned_cols=35 Identities=29% Similarity=0.498 Sum_probs=29.8
Q ss_pred CCCceEEEEEeeCCceeEEeccCchHHHHHHhhcC
Q 009012 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETG 170 (546)
Q Consensus 136 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg 170 (546)
....+.+.|.|..+-+|.||||+|.+|+.|+.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34557899999999999999999999999987543
No 84
>PRK00468 hypothetical protein; Provisional
Probab=95.34 E-value=0.031 Score=44.24 Aligned_cols=35 Identities=37% Similarity=0.634 Sum_probs=30.1
Q ss_pred CCCCceEEEEEeeCCceeEEeccCchHHHHHHhhc
Q 009012 135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 135 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~t 169 (546)
+....+.++|.|..+-+|.||||+|.+|+.|+.--
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 34566889999999999999999999999998643
No 85
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.31 E-value=0.018 Score=61.76 Aligned_cols=94 Identities=23% Similarity=0.318 Sum_probs=62.3
Q ss_pred ccceEecCCcHHHHHHHHHh-CCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhhhcCC
Q 009012 53 KIGSIIGRGGEIVKQLRIDT-KSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEELRGD 131 (546)
Q Consensus 53 ~vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~~~~~ 131 (546)
-+|..||++|++|+.|.++. |=+|.|-.- .-.+. . .+...+.-..+..-
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~-----------s~d~~----------------~---fi~nal~pa~v~~v 295 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILW-----------SDDPA----------------Q---FIINALSPAEVSSV 295 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEc-----------CCCHH----------------H---HHHHhCCCCEEEEE
Confidence 48999999999999999998 777775211 11100 0 01110000000000
Q ss_pred CCCCCCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 132 EDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 132 ~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
- -....-.+.+.||..+.+..|||+|++|+-....||.+|.|...
T Consensus 296 ~--~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 296 V--VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred E--EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 0 00012368899999999999999999999999999999999764
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.20 E-value=0.044 Score=58.91 Aligned_cols=93 Identities=24% Similarity=0.388 Sum_probs=64.4
Q ss_pred CcccccccCCchhHHHHHhhh-CCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccc--cccccCCcc
Q 009012 293 ANIGGVIGKGGAIINQIRQES-GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEK--IERDSGLIS 369 (546)
Q Consensus 293 ~~~g~iIGk~G~~Ik~i~~~s-ga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~--~~~~~~~~~ 369 (546)
+-+|..||++|++|+.|..+. |-+|.|-.-+.+ . ..-+..++ .|.-... +..+ .
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d---~--------------~~fi~nal--~pa~v~~v~~~~~----~ 301 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDD---P--------------AQFIINAL--SPAEVSSVVVDED----E 301 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC---H--------------HHHHHHhC--CCCEEEEEEEeCC----C
Confidence 458999999999999999998 777766543221 0 00111111 1111111 1111 2
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecC
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (546)
-...+.||....+..|||+|.+|+-..+.||.+|.|...
T Consensus 302 ~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 302 HSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred CEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 367899999999999999999999999999999999764
No 87
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.07 E-value=0.046 Score=43.08 Aligned_cols=33 Identities=42% Similarity=0.658 Sum_probs=29.8
Q ss_pred CCCceEEEEEeeCCceeEEeccCchHHHHHHhh
Q 009012 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSE 168 (546)
Q Consensus 136 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~ 168 (546)
......++|.|...-+|.||||+|.+|+.|+.-
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 467788999999999999999999999999864
No 88
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.06 E-value=0.56 Score=45.00 Aligned_cols=64 Identities=19% Similarity=0.377 Sum_probs=55.1
Q ss_pred EEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009012 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (546)
Q Consensus 141 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 214 (546)
.+.+.++....-.|...+|..+++|....||+|.+..+ +..|.|+|+...+..+...|.+++..
T Consensus 27 ~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 27 DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIRITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEEEEccHHHHHHHHHHHHHHHhh
Confidence 34555668889999999999999999999999999764 56899999999999999999888855
No 89
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=94.84 E-value=0.041 Score=53.86 Aligned_cols=63 Identities=21% Similarity=0.289 Sum_probs=52.5
Q ss_pred EEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCH-HHHHHHHHHHHHHHhcC
Q 009012 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEA-SVVKKALCQIASRLHDN 215 (546)
Q Consensus 142 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~-~~V~~A~~~I~~~l~~~ 215 (546)
+.+.||..+++.+||++|.+|+.|.++|+++|.|-. +-.|.|.+.. +++.+|+.+|..+-++.
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 568899999999999999999999999999998843 4568898864 57888888887766553
No 90
>PRK01064 hypothetical protein; Provisional
Probab=94.75 E-value=0.04 Score=43.86 Aligned_cols=33 Identities=27% Similarity=0.496 Sum_probs=29.6
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHh
Q 009012 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 40 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~t 72 (546)
.+.+.+++.|..+..|.+|||+|.+|+.||.-.
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 456789999999999999999999999999753
No 91
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.60 E-value=0.14 Score=55.87 Aligned_cols=67 Identities=21% Similarity=0.357 Sum_probs=49.5
Q ss_pred CceEEEEEeeC-CceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 138 ~~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
...+-.+.+|+ ++-|+||||.|.+|+.++.-||+.|-|... ...|+|++ +|---+-|...+..++.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt----------p~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----------PEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC----------CCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34455677887 578999999999999999999999988432 34678888 555555666666665544
No 92
>PRK01064 hypothetical protein; Provisional
Probab=94.60 E-value=0.079 Score=42.21 Aligned_cols=35 Identities=34% Similarity=0.595 Sum_probs=30.3
Q ss_pred CCCCceEEEEEeeCCceeEEeccCchHHHHHHhhc
Q 009012 135 DGGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 135 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~t 169 (546)
.....+.+++.|.....|.+|||+|.+|+.|+.-.
T Consensus 25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~ 59 (78)
T PRK01064 25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLL 59 (78)
T ss_pred eCCCEEEEEEEECcccceEEECCCCccHHHHHHHH
Confidence 34567889999999999999999999999998743
No 93
>PRK12704 phosphodiesterase; Provisional
Probab=94.47 E-value=0.15 Score=55.72 Aligned_cols=66 Identities=21% Similarity=0.348 Sum_probs=47.8
Q ss_pred ceEEEEEeeC-CceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 139 ~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
..+-.+.+|+ ++-|+||||.|.+|+.++.-||+.|-|... ..+|.|+| ++---+.|...+..++.+
T Consensus 209 ~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt----------p~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 209 TTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT----------PEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred hceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC----------CCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3445567787 578999999999999999999999988432 34688988 454444555555555543
No 94
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.46 E-value=0.046 Score=43.09 Aligned_cols=33 Identities=15% Similarity=0.343 Sum_probs=29.4
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHh
Q 009012 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 40 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~t 72 (546)
...+.++|-+..+.+|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 456789999999999999999999999999653
No 95
>PRK00106 hypothetical protein; Provisional
Probab=94.41 E-value=0.19 Score=54.85 Aligned_cols=67 Identities=25% Similarity=0.400 Sum_probs=50.2
Q ss_pred CceEEEEEeeC-CceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 138 ~~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
...+-.+.+|+ ++-|+||||.|.+|+.++.-||+.|-|... ...|.|++ +|---+-|...+..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt----------p~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT----------PEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC----------CCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34455677888 578999999999999999999999988432 34688888 565556666666666644
No 96
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=92.64 E-value=0.59 Score=52.90 Aligned_cols=28 Identities=21% Similarity=0.237 Sum_probs=12.7
Q ss_pred cEEEEEEeecCcccccccCCchhHHHHH
Q 009012 283 EFSLRLVCPVANIGGVIGKGGAIINQIR 310 (546)
Q Consensus 283 ~~~~~v~vp~~~~g~iIGk~G~~Ik~i~ 310 (546)
++..++-......-.+.+..-+.|..|+
T Consensus 935 efc~r~~l~~~~~~~t~~a~~ql~d~L~ 962 (1282)
T KOG0921|consen 935 EFCERYSLSNPVLKMTDGARRQLIDVLR 962 (1282)
T ss_pred hHhHhhhhcchhhhhhhhhHHHHHHHHH
Confidence 3344444444444444444444444455
No 97
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=92.59 E-value=0.062 Score=42.27 Aligned_cols=34 Identities=15% Similarity=0.214 Sum_probs=29.5
Q ss_pred CCceEEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009012 40 PEDTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 40 ~~~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tg 73 (546)
.+...+.+.|..+..|.||||+|.+++.||.-.+
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 4566788899999999999999999999996654
No 98
>PRK12705 hypothetical protein; Provisional
Probab=92.55 E-value=0.17 Score=54.87 Aligned_cols=38 Identities=24% Similarity=0.345 Sum_probs=32.9
Q ss_pred ceeEEEEEcCC-cceeEEcCCChhHHHHHHhcCceEEEe
Q 009012 369 SFTTRLLVPTS-RIGCLIGKGGSIITEMRRLTKANIRIL 406 (546)
Q Consensus 369 ~~~~~l~VP~~-~vG~IIGkgG~~Ik~I~~~tga~I~i~ 406 (546)
.....+.+|++ +-|.||||-|.+|+-+...||+.|.|.
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid 235 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID 235 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEec
Confidence 45667888875 559999999999999999999999993
No 99
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.42 E-value=0.072 Score=60.85 Aligned_cols=70 Identities=19% Similarity=0.109 Sum_probs=58.0
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHhc
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 445 (546)
-.+.+|.....+|||++|.+|+.++.-|||.|.|..- -|. ...||.+.+.|.++.++.|...|...|.+-
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~Dp 1411 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD--NQAERSKAPKGRPPSQRVATSPIGLPIIDP 1411 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc--cchhhhcccCCCChhhhhhhccccceeecC
Confidence 4577888889999999999999999999999999541 122 256899999999999999988887666554
No 100
>PRK12705 hypothetical protein; Provisional
Probab=89.69 E-value=0.77 Score=49.82 Aligned_cols=66 Identities=27% Similarity=0.358 Sum_probs=43.7
Q ss_pred ceEEEEEeeCC-ceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEc-CHHHHHHHHHHHHHHHhc
Q 009012 139 QVTAKLLVPSD-QIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISG-EASVVKKALCQIASRLHD 214 (546)
Q Consensus 139 ~~~~~llVp~~-~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G-~~~~V~~A~~~I~~~l~~ 214 (546)
...-.+-+|++ +-|+|||+.|.+|+.++..||+.|-|... | +.|.|++ ++..-+.|...+..+|..
T Consensus 197 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt---p-------~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 197 LSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT---P-------EAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred heeeeeecCChHhhccccCccchhHHHHHHhhCCceEecCC---c-------cchhhcccCccchHHHHHHHHHHHhc
Confidence 34445667774 67999999999999999999999988432 2 2355555 333334444444444433
No 101
>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=89.60 E-value=0.58 Score=35.53 Aligned_cols=35 Identities=14% Similarity=0.214 Sum_probs=28.1
Q ss_pred ceEEEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009012 42 DTVYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 42 ~~~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 76 (546)
.....+.+.....|.+||++|++|+.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35556666666789999999999999999987544
No 102
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=89.44 E-value=1.5 Score=49.72 Aligned_cols=6 Identities=83% Similarity=1.675 Sum_probs=2.4
Q ss_pred CCCCCC
Q 009012 490 GGYGSS 495 (546)
Q Consensus 490 ~Gyg~~ 495 (546)
||||++
T Consensus 1206 GGYGgs 1211 (1282)
T KOG0921|consen 1206 GGYGGS 1211 (1282)
T ss_pred CCCCCC
Confidence 444333
No 103
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=89.37 E-value=0.18 Score=46.75 Aligned_cols=55 Identities=24% Similarity=0.347 Sum_probs=49.2
Q ss_pred CCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009012 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 378 ~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 444 (546)
+..+|.|+||+|.+---|...|.++|.+. +..|.|-|..++++.|...|+.+|-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhcc
Confidence 45789999999999999999999999884 24799999999999999999998854
No 104
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.39 E-value=0.73 Score=49.39 Aligned_cols=68 Identities=19% Similarity=0.207 Sum_probs=56.5
Q ss_pred CCcceeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEc-CHHHHHHHHHHHHHHHHh
Q 009012 366 GLISFTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISG-DLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 366 ~~~~~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 444 (546)
....+..+|.|+.+..-.+||.+|-..|.|..+||+.-.+ ++.+|.|.- ++.+.++|+++|...+..
T Consensus 593 ~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 593 EYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DEGTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cCceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 3456788999999999999999999999999999965554 345788777 678889999999888776
Q ss_pred c
Q 009012 445 N 445 (546)
Q Consensus 445 ~ 445 (546)
+
T Consensus 661 ~ 661 (760)
T KOG1067|consen 661 D 661 (760)
T ss_pred c
Confidence 4
No 105
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=88.26 E-value=0.93 Score=47.78 Aligned_cols=40 Identities=35% Similarity=0.475 Sum_probs=36.3
Q ss_pred eEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCC
Q 009012 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (546)
Q Consensus 140 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (546)
-...+.||...++.+|||+|.+|++|+.+.|-+|.|...+
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 3477899999999999999999999999999999997653
No 106
>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=88.03 E-value=0.77 Score=34.80 Aligned_cols=35 Identities=26% Similarity=0.401 Sum_probs=28.5
Q ss_pred ceEEEEEeeCCceeEEeccCchHHHHHHhhcCceE
Q 009012 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQI 173 (546)
Q Consensus 139 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I 173 (546)
...+.+.+.....+.+|||+|++++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45566667666789999999999999999988554
No 107
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=87.20 E-value=2.6 Score=37.63 Aligned_cols=92 Identities=25% Similarity=0.413 Sum_probs=57.9
Q ss_pred CCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHh-hhcCCCCCCCCC
Q 009012 60 RGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE-ELRGDEDSDGGH 138 (546)
Q Consensus 60 k~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~-~~~~~~~~~~~~ 138 (546)
.+|+.|++|-++..-+|.|-. .+.. +.+-.+|...|.+.+-++ .+.+ -.-.
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~--------------dps~----------l~~~e~A~~~I~~ivP~ea~i~d----i~Fd 74 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRP--------------DPSV----------LKPPEEAIKIILEIVPEEAGITD----IYFD 74 (145)
T ss_pred cccHHHHHHHHHHhceEEEcC--------------Chhh----------cCCHHHHHHHHHHhCCCccCcee----eEec
Confidence 568899999999988887621 1110 111234554444432111 1110 0001
Q ss_pred ceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCC
Q 009012 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDE 179 (546)
Q Consensus 139 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 179 (546)
..+-.+.|-...-|.+|||+|.++++|..+||-.-.|....
T Consensus 75 ~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtp 115 (145)
T cd02410 75 DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTP 115 (145)
T ss_pred CCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecC
Confidence 22355667778889999999999999999999999887753
No 108
>PRK13764 ATPase; Provisional
Probab=86.94 E-value=1.2 Score=49.49 Aligned_cols=43 Identities=28% Similarity=0.470 Sum_probs=38.8
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCC
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLP 412 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P 412 (546)
-...+.||.+.++.+|||+|.+|++|.++.|.+|.|...++.|
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4567999999999999999999999999999999998776654
No 109
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.92 E-value=0.43 Score=37.12 Aligned_cols=37 Identities=27% Similarity=0.436 Sum_probs=29.7
Q ss_pred eEEEEEcCCc-----ceeEEcCCChhHHHHHHhc-CceEEEec
Q 009012 371 TTRLLVPTSR-----IGCLIGKGGSIITEMRRLT-KANIRILP 407 (546)
Q Consensus 371 ~~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~t-ga~I~i~~ 407 (546)
...+.|-... +|..||++|.+|+.|.++. |-+|+|-.
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 3556777777 8999999999999999999 89998854
No 110
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=86.67 E-value=0.29 Score=38.45 Aligned_cols=34 Identities=21% Similarity=0.311 Sum_probs=28.6
Q ss_pred CceEEEEEeeCCceeEEeccCchHHHHHHhhcCc
Q 009012 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGA 171 (546)
Q Consensus 138 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga 171 (546)
....+.+-+..+..|.||||.|.|++.||.-.++
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 4456788889999999999999999999876544
No 111
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=86.47 E-value=2.7 Score=44.68 Aligned_cols=152 Identities=18% Similarity=0.227 Sum_probs=101.3
Q ss_pred ceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCCCC
Q 009012 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNPSR 218 (546)
Q Consensus 139 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~~~ 218 (546)
...+.+.+|...+..|||.+|..|+++..+.++.|++...-+++. + .-+
T Consensus 448 pae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s-----------------------~~~----- 496 (657)
T COG5166 448 PAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---S-----------------------QWH----- 496 (657)
T ss_pred chheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---h-----------------------hhh-----
Confidence 345789999999999999999999999999998887754322221 0 000
Q ss_pred cchhhcccccCCCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEEEeecCccccc
Q 009012 219 SQHLLASAISNSHSSSGSLVGPTAATPIVGIAPLMGPYGGYKGDTAGDWSRSLYSAPRDDLSSKEFSLRLVCPVANIGGV 298 (546)
Q Consensus 219 ~~~~~~~~~~~~~~~gg~~~~p~~g~~~~~~~p~~~~~gg~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~vp~~~~g~i 298 (546)
..+-+.+|.+..+.|
T Consensus 497 -----------------------------------------------------------------dNV~I~~PrKn~~ni 511 (657)
T COG5166 497 -----------------------------------------------------------------DNVLIEAPRKNQDNI 511 (657)
T ss_pred -----------------------------------------------------------------cceEEECCccCccch
Confidence 024567888889999
Q ss_pred ccCCchhHHHHHhhh----CCeEEecCCCCCCCceEEEEecCcchhhhchHHHHHHHHhcCccccccccccCCcceeEEE
Q 009012 299 IGKGGAIINQIRQES----GAAIKVDSSSTEGDDCLITVSSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRL 374 (546)
Q Consensus 299 IGk~G~~Ik~i~~~s----ga~I~i~~~~~~~~~rvi~I~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l 374 (546)
+|++......+++.+ ...|.+... ..++.++.+-.. .++.++.- +.+- ......+.+
T Consensus 512 ~~~KNd~~~~V~~~c~f~~Kgdirf~~~----~~sI~~v~~~~~-------~I~rv~kn-----e~v~---~~~p~~~~~ 572 (657)
T COG5166 512 SGKKNDKLDKVKQQCRFNLKGDIRFCPQ----STSIFTVDIYSD-------EIERVIKN-----ETVL---LEFPAEMHF 572 (657)
T ss_pred hcccccHHHHHhhhcccccccceEEcCC----ceEEEEEccccc-------HHHHHhhc-----cceE---Eeccccccc
Confidence 999988888888665 234444432 345777776432 23333321 0000 011345668
Q ss_pred EEcCCcceeEEc---CCChhHHHHHHhcCceEEE
Q 009012 375 LVPTSRIGCLIG---KGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 375 ~VP~~~vG~IIG---kgG~~Ik~I~~~tga~I~i 405 (546)
.+|+..++.-+| -.|++|..+.....-.|..
T Consensus 573 y~~se~h~~g~gena~R~~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 573 YVPSEIHKKGIGENAFRGENIQRVTKLYNSYIEF 606 (657)
T ss_pred ccchhhhhccCCcccccccchhhhhhhhhcccee
Confidence 899999999999 7788888887776666654
No 112
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=85.97 E-value=0.8 Score=36.39 Aligned_cols=32 Identities=19% Similarity=0.255 Sum_probs=26.0
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 76 (546)
+.+.+..+..|.+|||+|+++..||--++.-+
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 45666678899999999999999997766443
No 113
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.39 E-value=0.53 Score=43.74 Aligned_cols=57 Identities=28% Similarity=0.394 Sum_probs=50.3
Q ss_pred CCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcCC
Q 009012 148 SDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDNP 216 (546)
Q Consensus 148 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~~ 216 (546)
+..+|+|+||+|.|--.|+.-|.++|.+. +..|.|-|..++++-|...|+.+|...+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVla------------d~kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLA------------DSKIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEec------------CceEEEeecchhhHHHHHhhHhhhccCC
Confidence 45789999999999999999999999774 4469999999999999999999997653
No 114
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=85.36 E-value=2.1 Score=45.59 Aligned_cols=127 Identities=24% Similarity=0.407 Sum_probs=75.7
Q ss_pred EecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHhh-hcCCCCCC
Q 009012 57 IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAEE-LRGDEDSD 135 (546)
Q Consensus 57 IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~~-~~~~~~~~ 135 (546)
+|=+.|..|++|.++..-+|.|-.. +.. +.+..+|...|++-+-++. +.+ -
T Consensus 43 ~~~~~~dlik~lAk~lrKRI~iR~d--------------Psv----------l~~~e~A~~~I~eivP~ea~i~~----i 94 (637)
T COG1782 43 LFAKDGDLIKDLAKDLRKRIIIRPD--------------PSV----------LKPPEEARKIILEIVPEEAGITD----I 94 (637)
T ss_pred HhccchhHHHHHHHHHhhceEeccC--------------chh----------cCCHHHHHHHHHHhCccccCcee----E
Confidence 4557889999999999888876321 111 2223566655555332211 110 0
Q ss_pred CCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEE----EcCHHHHHHHHHHHHHH
Q 009012 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQI----SGEASVVKKALCQIASR 211 (546)
Q Consensus 136 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I----~G~~~~V~~A~~~I~~~ 211 (546)
.-...+-.++|-...-|.||||+|++.++|..+||-.-.|.+...++. .-+..| .-..+..++.+..|-..
T Consensus 95 ~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PPi~S-----~ti~~ir~~l~~~~~eR~~iL~~vg~r 169 (637)
T COG1782 95 YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPPIQS-----RTIKSIREILRSERKERREILRNVGRR 169 (637)
T ss_pred EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCCCch-----hhHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 112234667888899999999999999999999998888877533221 111111 22334444555666666
Q ss_pred HhcCC
Q 009012 212 LHDNP 216 (546)
Q Consensus 212 l~~~~ 216 (546)
|+..+
T Consensus 170 Ihr~~ 174 (637)
T COG1782 170 IHREP 174 (637)
T ss_pred hcCCc
Confidence 65543
No 115
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=84.24 E-value=0.3 Score=56.09 Aligned_cols=71 Identities=27% Similarity=0.247 Sum_probs=58.7
Q ss_pred eEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009012 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (546)
Q Consensus 140 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 214 (546)
...++-+|-....+|||++|.+|+.++.-|||-|.|.+-. + .+-.+|.+.+.|.++.++-|...|.-.+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq--~--~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQ--P--DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcC--C--ccchhhhcccCCCChhhhhhhccccceeec
Confidence 3467788999999999999999999999999999996621 1 124689999999999999998888766644
No 116
>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=84.11 E-value=1.1 Score=35.52 Aligned_cols=34 Identities=24% Similarity=0.459 Sum_probs=27.6
Q ss_pred EEEEEeeCCceeEEeccCchHHHHHHhhcCceEE
Q 009012 141 TAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIR 174 (546)
Q Consensus 141 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~ 174 (546)
.+.+-|..+..|.||||.|+++..||--+..-++
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 4567777889999999999999999887665443
No 117
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=84.04 E-value=1.7 Score=42.56 Aligned_cols=51 Identities=16% Similarity=0.185 Sum_probs=45.0
Q ss_pred eEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhc
Q 009012 152 GCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHD 214 (546)
Q Consensus 152 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~ 214 (546)
-+|||.+|+|++.|+-.|.|-|-|.. .+|.+.|....+..+...|.+.+..
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 58999999999999999999998853 3699999999999888888888865
No 118
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=83.90 E-value=0.6 Score=36.34 Aligned_cols=37 Identities=32% Similarity=0.572 Sum_probs=29.7
Q ss_pred EEEEeeCCc-----eeEEeccCchHHHHHHhhc-CceEEEecC
Q 009012 142 AKLLVPSDQ-----IGCVIGKGGQIVQNIRSET-GAQIRILKD 178 (546)
Q Consensus 142 ~~llVp~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~ 178 (546)
+++.|-+.. +|..||++|.+|+.|.++. |-+|+|...
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~ 47 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEY 47 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE-
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEc
Confidence 556666666 8999999999999999999 999999764
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=83.55 E-value=2.6 Score=40.81 Aligned_cols=58 Identities=22% Similarity=0.406 Sum_probs=44.9
Q ss_pred EEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHH-HHHHHHHHHH
Q 009012 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASV-VKKALCQIAS 210 (546)
Q Consensus 142 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~-V~~A~~~I~~ 210 (546)
.-+.||+..+.++||++|+.++-|.++|+|+|-|-. .-.|-|.+..+. ...|..+|..
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~~~e~~~~~aI~~ 206 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENESLEELAIEAIRK 206 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCcchHHHHHHHHHH
Confidence 446789999999999999999999999999998854 345777777664 4444444444
No 120
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=83.15 E-value=4 Score=40.73 Aligned_cols=22 Identities=41% Similarity=0.952 Sum_probs=9.2
Q ss_pred CCCCCCCCCCCCCCCCCCCCCC
Q 009012 504 GSYGSSQLGGTGSAYGSYGSYS 525 (546)
Q Consensus 504 g~~G~~~~~~~g~~yg~~g~~~ 525 (546)
|.||++.+|+-|++|..+++|+
T Consensus 79 g~YGgGygg~fGgGyN~~~~~g 100 (362)
T KOG3875|consen 79 GPYGGGYGGGFGGGYNRFGPYG 100 (362)
T ss_pred CCcCCCcCcccCcccccccccc
Confidence 3343333333344444444444
No 121
>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=82.86 E-value=1.2 Score=35.80 Aligned_cols=36 Identities=11% Similarity=0.280 Sum_probs=30.9
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcC
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGE 80 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~ 80 (546)
.++.|....-|.|||++|+.|++|+++-.-...+.+
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~ 67 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPE 67 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCC
Confidence 788899999999999999999999998876665533
No 122
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=82.53 E-value=0.65 Score=36.89 Aligned_cols=33 Identities=18% Similarity=0.381 Sum_probs=28.6
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009012 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 44 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 76 (546)
...+.+.....+.|||++|++|++|..+..-.+
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 367888999999999999999999998876555
No 123
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.43 E-value=0.84 Score=48.09 Aligned_cols=40 Identities=33% Similarity=0.475 Sum_probs=36.2
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCC
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKEN 410 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~ 410 (546)
...+.||..+++.||||+|.+|++|.++.|-+|.|...+.
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 4668999999999999999999999999999999976543
No 124
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=81.93 E-value=2.6 Score=41.35 Aligned_cols=51 Identities=24% Similarity=0.261 Sum_probs=43.3
Q ss_pred eeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHHh
Q 009012 382 GCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLRA 444 (546)
Q Consensus 382 G~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 444 (546)
-.+||.+|.+++.|+-.|.|.|-|+. .+|.+.|....++.+...+.+.+.+
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 57899999999999999999999964 3899999988888887777666654
No 125
>PRK13764 ATPase; Provisional
Probab=81.80 E-value=3.1 Score=46.29 Aligned_cols=45 Identities=31% Similarity=0.499 Sum_probs=39.0
Q ss_pred CceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCC
Q 009012 138 HQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLP 182 (546)
Q Consensus 138 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p 182 (546)
..-...+.||...++.+|||+|.+|++|+++.|..|.|...++.+
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 344578899999999999999999999999999999998765433
No 126
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=81.01 E-value=3.7 Score=39.75 Aligned_cols=47 Identities=21% Similarity=0.408 Sum_probs=39.1
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHH
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLD 429 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~ 429 (546)
+-+.||+..|-.+||++|+.++-+.+.|+|+|-|-.. -.|-|.+..+
T Consensus 148 ~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N-----------G~IWV~~~~~ 194 (239)
T COG1097 148 QIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN-----------GRIWVDGENE 194 (239)
T ss_pred EEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC-----------CEEEecCCCc
Confidence 4588999999999999999999999999999998542 3566666544
No 127
>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=79.22 E-value=0.72 Score=36.62 Aligned_cols=34 Identities=29% Similarity=0.474 Sum_probs=28.7
Q ss_pred eEEEEEeeCCceeEEeccCchHHHHHHhhcCceE
Q 009012 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQI 173 (546)
Q Consensus 140 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I 173 (546)
..+.+.+...+.+.|||++|++|++|.+...-.+
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 3467888899999999999999999988766555
No 128
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=79.21 E-value=2.5 Score=38.78 Aligned_cols=33 Identities=30% Similarity=0.386 Sum_probs=28.1
Q ss_pred EEEecCCccceEecCCcHHHHHHHHHhCCeEEEc
Q 009012 46 RYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIG 79 (546)
Q Consensus 46 rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 79 (546)
-++|-... |.-|||+|++|++|++..|-+|.|-
T Consensus 64 IfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 64 ILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 45565566 9999999999999999999999863
No 129
>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=78.15 E-value=2.7 Score=33.77 Aligned_cols=35 Identities=20% Similarity=0.446 Sum_probs=28.9
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEE
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRI 405 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i 405 (546)
.+++.|....-|.|||++|+.|++|++.-.....+
T Consensus 31 ~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~ 65 (81)
T cd02413 31 RTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNF 65 (81)
T ss_pred eEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCC
Confidence 46788888899999999999999999876554444
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=77.34 E-value=3.3 Score=38.02 Aligned_cols=36 Identities=33% Similarity=0.611 Sum_probs=31.7
Q ss_pred EEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecC
Q 009012 142 AKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKD 178 (546)
Q Consensus 142 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 178 (546)
+-++|-... |..|||+|.+|+.+++..|-+|.|...
T Consensus 63 vIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 63 VILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 667776666 999999999999999999999999764
No 131
>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=74.52 E-value=4.6 Score=36.07 Aligned_cols=37 Identities=22% Similarity=0.362 Sum_probs=31.4
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCC
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET 81 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 81 (546)
=.+.|-.+.-|.+|||+|.+++.|..+||-+-.|-..
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 3577788899999999999999999999987766433
No 132
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=71.43 E-value=7.6 Score=43.73 Aligned_cols=96 Identities=24% Similarity=0.426 Sum_probs=60.3
Q ss_pred EecCCcHHHHHHHHHhCCeEEEcCCCCCCcceEEEEecCCccccccccCcccCCHHHHHHHHHHHHHHHh-hhcCCCCCC
Q 009012 57 IIGRGGEIVKQLRIDTKSKIRIGETVPGSEERVVTVYSASDETNAFEDGDKFVSPAQDALFKVHDRVIAE-ELRGDEDSD 135 (546)
Q Consensus 57 IIGk~G~~Ik~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~e~~~~~v~~a~~a~~~i~~~i~~~-~~~~~~~~~ 135 (546)
.+=.+++.|++|-++-.-+|.|-.. +.- +.+..+|.+.|.+.+-++ .+.+ -
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~--------------~~~----------~~~~~~~~~~i~~~~~~~~~~~~----~ 88 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPD--------------PSV----------LLPPEEAIEKIKEIVPEEAGITD----I 88 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecC--------------hhh----------cCCHHHHHHHHHHhCCCcCCcee----E
Confidence 3446789999999998888766211 110 111234544444422111 1100 0
Q ss_pred CCCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCC
Q 009012 136 GGHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEH 180 (546)
Q Consensus 136 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~ 180 (546)
.-...+-.++|-...-|.||||+|.++++|..+||-+-.|.+...
T Consensus 89 ~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 89 YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred EecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 012234567778888999999999999999999999999987633
No 133
>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=71.11 E-value=3.9 Score=34.88 Aligned_cols=31 Identities=23% Similarity=0.324 Sum_probs=26.6
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCe
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~ 75 (546)
+++.|-...-|.|||++|++|++|++.....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 6788888889999999999999999876543
No 134
>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=67.75 E-value=6.1 Score=31.98 Aligned_cols=28 Identities=25% Similarity=0.380 Sum_probs=23.7
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHh
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDT 72 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~t 72 (546)
.++.|....-|.+||++|.+|++|+..-
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 5566666889999999999999999775
No 135
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=64.98 E-value=11 Score=40.29 Aligned_cols=130 Identities=14% Similarity=0.103 Sum_probs=80.0
Q ss_pred cccccCCchhHHHHHhhhCCeEEecCCCCCCCceEEEE-ecCcchhhhchHHHHHHHHhcCccccccccccCCcceeEEE
Q 009012 296 GGVIGKGGAIINQIRQESGAAIKVDSSSTEGDDCLITV-SSKEFFEDTLSATIEAVVRLQPRCSEKIERDSGLISFTTRL 374 (546)
Q Consensus 296 g~iIGk~G~~Ik~i~~~sga~I~i~~~~~~~~~rvi~I-~G~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~l 374 (546)
-++-||+..++.+|++..-|.+.+.=.... +.++.++ .|. .+.....+...+ . .-.....+
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~-gs~~~~~~~g~-------~~~F~k~~~~~~-------~---EFpae~~f 453 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST-GSIVETNGIGE-------KMSFSKKLSIPP-------T---EFPAEIAF 453 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC-CcEEEEeccCc-------chhhHHHhcCCc-------c---cCchheEE
Confidence 478888888899999988887443321111 1233332 222 112222222111 0 11245679
Q ss_pred EEcCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcC---HHHHHHHHHHHHHHHHhc
Q 009012 375 LVPTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGD---LDLAKDALIQVMTRLRAN 445 (546)
Q Consensus 375 ~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~---~~~v~~A~~~I~~~l~~~ 445 (546)
.||...|..|||-||..|+++...-++.|+....-++|....-+ -|.|.-+ .+++.-++.-+.+++.+.
T Consensus 454 ~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~~d--NV~I~~PrKn~~ni~~~KNd~~~~V~~~ 525 (657)
T COG5166 454 IIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQWHD--NVLIEAPRKNQDNISGKKNDKLDKVKQQ 525 (657)
T ss_pred EeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhhhc--ceEEECCccCccchhcccccHHHHHhhh
Confidence 99999999999999999999999999999987666666532211 2556553 345555666666666654
No 136
>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=64.91 E-value=7.4 Score=31.49 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=22.9
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhc
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~t 399 (546)
..+.|....-|.+||++|++|++|++.-
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 4566666788999999999999998764
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=64.01 E-value=6.2 Score=38.10 Aligned_cols=31 Identities=23% Similarity=0.351 Sum_probs=26.8
Q ss_pred eEEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009012 43 TVYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 43 ~~~rilip~~~vg~IIGk~G~~Ik~I~~~tg 73 (546)
...++.|....-|.||||+|+.|++|+++..
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 3467889999999999999999999997654
No 138
>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=63.76 E-value=6.3 Score=33.60 Aligned_cols=29 Identities=31% Similarity=0.524 Sum_probs=24.6
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcC
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tg 400 (546)
.++.|-...-|.|||+.|+.|++|++...
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 56777788889999999999999987644
No 139
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=61.91 E-value=7.5 Score=37.56 Aligned_cols=29 Identities=38% Similarity=0.543 Sum_probs=25.1
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHh
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRL 398 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~ 398 (546)
..+++.|....-|.|||++|+.|++|++.
T Consensus 51 ~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 51 KGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 45778888999999999999999998753
No 140
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=59.04 E-value=27 Score=37.60 Aligned_cols=39 Identities=28% Similarity=0.416 Sum_probs=33.4
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecC
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (546)
.+-++.|-.+.-|.||||+|++.++|.++||-.-+|.+.
T Consensus 99 ~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 99 DTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred CCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 345688889999999999999999999999987777653
No 141
>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=53.17 E-value=16 Score=36.29 Aligned_cols=31 Identities=23% Similarity=0.318 Sum_probs=25.4
Q ss_pred ceeEEEEEcCCcc-eeEEcCCChhHHHHHHhc
Q 009012 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 369 ~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~t 399 (546)
.+...+.|..+-+ +.|||++|+.||+|...+
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 4777888886655 999999999999987654
No 142
>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=50.05 E-value=19 Score=35.85 Aligned_cols=31 Identities=26% Similarity=0.427 Sum_probs=24.5
Q ss_pred ceEEEEEeeC-CceeEEeccCchHHHHHHhhc
Q 009012 139 QVTAKLLVPS-DQIGCVIGKGGQIVQNIRSET 169 (546)
Q Consensus 139 ~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~t 169 (546)
.+...++|.. ++-+.||||+|++||+|..+.
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 3667778885 578999999999999875543
No 143
>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=49.85 E-value=35 Score=38.48 Aligned_cols=39 Identities=26% Similarity=0.455 Sum_probs=34.2
Q ss_pred eeEEEEEcCCcceeEEcCCChhHHHHHHhcCceEEEecC
Q 009012 370 FTTRLLVPTSRIGCLIGKGGSIITEMRRLTKANIRILPK 408 (546)
Q Consensus 370 ~~~~l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~ 408 (546)
.+-++.|-.+.-|.||||+|.++++|.++||-+-+|.+.
T Consensus 93 ~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~ 131 (630)
T TIGR03675 93 VTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRT 131 (630)
T ss_pred CCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEec
Confidence 456788889999999999999999999999988888653
No 144
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=49.82 E-value=35 Score=25.76 Aligned_cols=40 Identities=10% Similarity=0.047 Sum_probs=27.1
Q ss_pred HHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHH
Q 009012 396 RRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMT 440 (546)
Q Consensus 396 ~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 440 (546)
.+.+++.| +.....+|. ..-.+.|+|+.++|+.|+..|.+
T Consensus 20 ~Kaa~V~i-~d~f~gCPq----~~~~l~i~Gdvs~Ve~Al~~i~~ 59 (61)
T cd07055 20 EKASGVFV-SDIFGSCPQ----HMITLAIFGETSAVELAMREIEE 59 (61)
T ss_pred hhccCeEE-EEecCCCCC----ceEEEEEEecHHHHHHHHHHHhh
Confidence 34455666 444444453 34468899999999999988865
No 145
>COG1159 Era GTPase [General function prediction only]
Probab=48.30 E-value=20 Score=36.13 Aligned_cols=30 Identities=30% Similarity=0.591 Sum_probs=23.6
Q ss_pred CceEEEEEeeC-CceeEEeccCchHHHHHHh
Q 009012 138 HQVTAKLLVPS-DQIGCVIGKGGQIVQNIRS 167 (546)
Q Consensus 138 ~~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~ 167 (546)
-.+...++|+. +|-+.||||+|++||+|-.
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~ 257 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGT 257 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHH
Confidence 34566778885 5889999999999988743
No 146
>COG1159 Era GTPase [General function prediction only]
Probab=47.85 E-value=14 Score=37.14 Aligned_cols=35 Identities=26% Similarity=0.544 Sum_probs=26.7
Q ss_pred cCCcceeEEEEEcCCcc-eeEEcCCChhHHHHHHhc
Q 009012 365 SGLISFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 365 ~~~~~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~t 399 (546)
.+...+...+.|+.+-. |-||||+|+.||+|-..+
T Consensus 224 ~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 224 KGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred CCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 33445677788887654 999999999999986554
No 147
>PRK15494 era GTPase Era; Provisional
Probab=47.39 E-value=22 Score=36.75 Aligned_cols=31 Identities=23% Similarity=0.382 Sum_probs=24.9
Q ss_pred ceeEEEEEcCCcc-eeEEcCCChhHHHHHHhc
Q 009012 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 369 ~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~t 399 (546)
.+...+.|..+-+ +.|||++|+.||+|..+.
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 4667888887655 999999999999886543
No 148
>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=45.27 E-value=4.8e+02 Score=29.10 Aligned_cols=62 Identities=24% Similarity=0.365 Sum_probs=36.6
Q ss_pred EEEEEeeCCceeEEeccCchHHHHHH------hhcCceEEEecCC--CCCc---ccCCCCceEEEEcCHHHHHHHHHHH
Q 009012 141 TAKLLVPSDQIGCVIGKGGQIVQNIR------SETGAQIRILKDE--HLPS---CALRSDELVQISGEASVVKKALCQI 208 (546)
Q Consensus 141 ~~~llVp~~~vg~IIGk~G~~Ik~I~------~~tga~I~i~~~~--~~p~---~~~~~dr~v~I~G~~~~V~~A~~~I 208 (546)
..++.+|+ ..++|| +++++. +..|+.|.-.... +++. .....-..+.+.|++++++++.+.+
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~l 376 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQL 376 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHc
Confidence 44455554 345555 788886 3678776554332 1221 1112234688999999999876653
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=44.66 E-value=26 Score=35.17 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=24.4
Q ss_pred ceeEEEEEcCCcc-eeEEcCCChhHHHHHHhc
Q 009012 369 SFTTRLLVPTSRI-GCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 369 ~~~~~l~VP~~~v-G~IIGkgG~~Ik~I~~~t 399 (546)
.+...+.|..+-+ +.|||++|+.||+|...+
T Consensus 225 ~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 225 RIEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 4677788886555 999999999999886543
No 150
>PRK15494 era GTPase Era; Provisional
Probab=44.56 E-value=25 Score=36.35 Aligned_cols=29 Identities=17% Similarity=0.415 Sum_probs=23.4
Q ss_pred eEEEEEeeC-CceeEEeccCchHHHHHHhh
Q 009012 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRSE 168 (546)
Q Consensus 140 ~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~ 168 (546)
+...|+|.. ++-+.||||+|++||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 567788885 57899999999999987543
No 151
>PRK00089 era GTPase Era; Reviewed
Probab=43.27 E-value=28 Score=34.98 Aligned_cols=29 Identities=38% Similarity=0.715 Sum_probs=22.8
Q ss_pred eEEEEEeeC-CceeEEeccCchHHHHHHhh
Q 009012 140 VTAKLLVPS-DQIGCVIGKGGQIVQNIRSE 168 (546)
Q Consensus 140 ~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~ 168 (546)
+...|.|.. ++.+.||||+|++||+|..+
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ 255 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTE 255 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHH
Confidence 566677774 57899999999999887543
No 152
>PRK03818 putative transporter; Validated
Probab=41.91 E-value=3.1e+02 Score=30.51 Aligned_cols=133 Identities=14% Similarity=0.235 Sum_probs=70.2
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeEEEcCC---------CCC---CcceEEEEecCCccccccccCcccCCHH
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIRIGET---------VPG---SEERVVTVYSASDETNAFEDGDKFVSPA 112 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~---------~~~---~~ervv~I~G~~e~~~~~e~~~~~v~~a 112 (546)
.++.|+++. ++ |++++++.......+.|..- .++ ....++.|.|..+
T Consensus 207 r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e--------------- 265 (552)
T PRK03818 207 INIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPE--------------- 265 (552)
T ss_pred EEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHH---------------
Confidence 566666443 34 67999999988777666311 111 1235677777644
Q ss_pred HHHHHHHHHHHHHhhhcCCCCCCCCCceEEEEEeeCCceeEEeccCchHHHHH--HhhcCceEEEecCC--CCCc---cc
Q 009012 113 QDALFKVHDRVIAEELRGDEDSDGGHQVTAKLLVPSDQIGCVIGKGGQIVQNI--RSETGAQIRILKDE--HLPS---CA 185 (546)
Q Consensus 113 ~~a~~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I--~~~tga~I~i~~~~--~~p~---~~ 185 (546)
++.++.+.+-.+. ..+.+..........+++|++ .++|| +++++ +++.|+.|.=.... +++. ..
T Consensus 266 --~l~~l~~~~Gl~~-~~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~~ 336 (552)
T PRK03818 266 --DLHKAQLVIGEEV-DTSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDLS 336 (552)
T ss_pred --HHHHHHHhcCCcc-CccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCCE
Confidence 3333333222110 000111122344555555553 56665 78877 56677765443321 2211 11
Q ss_pred CCCCceEEEEcCHHHHHHHHHH
Q 009012 186 LRSDELVQISGEASVVKKALCQ 207 (546)
Q Consensus 186 ~~~dr~v~I~G~~~~V~~A~~~ 207 (546)
...-.++.+.|+++++++..+.
T Consensus 337 Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 337 LQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred EecCCEEEEEECHHHHHHHHHH
Confidence 1223468899999999987664
No 153
>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=38.30 E-value=35 Score=32.36 Aligned_cols=30 Identities=23% Similarity=0.454 Sum_probs=26.2
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCC
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKS 74 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga 74 (546)
.++.|....-|.|||++|..|++|+++-.-
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 678888888999999999999999987643
No 154
>CHL00048 rps3 ribosomal protein S3
Probab=38.27 E-value=34 Score=32.96 Aligned_cols=30 Identities=17% Similarity=0.217 Sum_probs=25.8
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhC
Q 009012 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 44 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tg 73 (546)
..++.|-...-+.|||++|++|++|++.-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 467777788899999999999999998764
No 155
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.72 E-value=34 Score=32.72 Aligned_cols=31 Identities=29% Similarity=0.426 Sum_probs=25.3
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCe
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSK 75 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~ 75 (546)
.++.|....-|.+||++|++|++|++.-.-.
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 4556666889999999999999999886543
No 156
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=37.46 E-value=34 Score=34.75 Aligned_cols=37 Identities=24% Similarity=0.489 Sum_probs=28.3
Q ss_pred ccCCcceeEEEEEcCCc-ceeEEcCCChhHHHHHHhcC
Q 009012 364 DSGLISFTTRLLVPTSR-IGCLIGKGGSIITEMRRLTK 400 (546)
Q Consensus 364 ~~~~~~~~~~l~VP~~~-vG~IIGkgG~~Ik~I~~~tg 400 (546)
..+...+..++.+|... .-.||||+|..|++|-++.+
T Consensus 322 ~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~ 359 (379)
T KOG1423|consen 322 PAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRAN 359 (379)
T ss_pred CCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHH
Confidence 33445688889999764 47789999999999976543
No 157
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=36.68 E-value=28 Score=31.75 Aligned_cols=61 Identities=23% Similarity=0.268 Sum_probs=38.5
Q ss_pred EEEcCCcceeEEcCCChhHHHHHHhcCceE-EEecCCCC-----CCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009012 374 LLVPTSRIGCLIGKGGSIITEMRRLTKANI-RILPKENL-----PKIASEDDEMVQISGDLDLAKDALIQVM 439 (546)
Q Consensus 374 l~VP~~~vG~IIGkgG~~Ik~I~~~tga~I-~i~~~~~~-----P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 439 (546)
+..-+.++|+=||- -+|+++|||.| -|.+.+++ |...-....++.+.|+...+..++.+..
T Consensus 92 i~~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 92 IEAGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred eecCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 33334566666665 56799999884 44444331 2211233458999999999998876653
No 158
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=36.47 E-value=32 Score=32.72 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=30.2
Q ss_pred ceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEE
Q 009012 139 QVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRI 175 (546)
Q Consensus 139 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 175 (546)
.-.+.+-+..+..+.|||+.|.++..||--+.+-++-
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 3456677777889999999999999999988776643
No 159
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=36.20 E-value=25 Score=33.44 Aligned_cols=34 Identities=15% Similarity=0.171 Sum_probs=27.6
Q ss_pred EEEEEecCCccceEecCCcHHHHHHHHHhCCeEE
Q 009012 44 VYRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKIR 77 (546)
Q Consensus 44 ~~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I~ 77 (546)
.+.+-+-.+..+.+||+.|+++..||--+++-++
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~ 125 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLN 125 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhh
Confidence 4556667777999999999999999988775554
No 160
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=35.61 E-value=85 Score=32.38 Aligned_cols=51 Identities=18% Similarity=0.165 Sum_probs=42.6
Q ss_pred cCCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHH
Q 009012 377 PTSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVM 439 (546)
Q Consensus 377 P~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 439 (546)
+.+..-.|.|..+.+++.|.+..|+.|... .+.++|+|+.+.|..|...+.
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 356678899999999999999999998762 247999999778888877776
No 161
>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=35.38 E-value=40 Score=31.91 Aligned_cols=29 Identities=31% Similarity=0.560 Sum_probs=24.6
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhc
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~t 399 (546)
.+++.|....-|.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46788888888999999999999997653
No 162
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=34.14 E-value=41 Score=32.49 Aligned_cols=32 Identities=9% Similarity=0.253 Sum_probs=26.9
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhCCeE
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTKSKI 76 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tga~I 76 (546)
.++.|....-|.|||++|..|++|+++-.-.+
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 67778888899999999999999998865443
No 163
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=33.03 E-value=45 Score=31.94 Aligned_cols=29 Identities=34% Similarity=0.644 Sum_probs=23.5
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhcC
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLTK 400 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~tg 400 (546)
..+.|....-|.+||++|++|+++++.-.
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lk 70 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILE 70 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHH
Confidence 45566668889999999999999987653
No 164
>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=32.99 E-value=1.2e+02 Score=27.73 Aligned_cols=57 Identities=23% Similarity=0.234 Sum_probs=43.6
Q ss_pred CCceEEEEEeeCCceeEEeccCchHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHH
Q 009012 137 GHQVTAKLLVPSDQIGCVIGKGGQIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASR 211 (546)
Q Consensus 137 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~ 211 (546)
...-++|+-+|....- +.+++|.+-.|+-+.+ . .+..|.|.|..+.|.+|++.+..+
T Consensus 110 ~~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef-e----------e~~~V~I~Gdke~Ik~aLKe~s~~ 166 (169)
T PF09869_consen 110 PGFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF-E----------EDDKVVIEGDKERIKKALKEFSSF 166 (169)
T ss_pred CCceeEEEecCccchH-------HHHHHHHHHhceeEEe-c----------CCcEEEEeccHHHHHHHHHHHHHH
Confidence 3445666666665442 5678999999999988 2 255799999999999999998765
No 165
>CHL00048 rps3 ribosomal protein S3
Probab=32.64 E-value=46 Score=32.03 Aligned_cols=29 Identities=21% Similarity=0.169 Sum_probs=24.5
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhc
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~t 399 (546)
.+++.|-...-|.|||++|..|++|++.-
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677778888999999999999998764
No 166
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=32.41 E-value=45 Score=32.25 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=24.3
Q ss_pred eEEEEEcCCcceeEEcCCChhHHHHHHhc
Q 009012 371 TTRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 371 ~~~l~VP~~~vG~IIGkgG~~Ik~I~~~t 399 (546)
.+++.|....-|.|||++|..|++|++.-
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L 73 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLL 73 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHH
Confidence 36677778888999999999999997654
No 167
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=32.38 E-value=44 Score=33.94 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=27.3
Q ss_pred CCceEEEEEeeC-CceeEEeccCchHHHHHHhhcC
Q 009012 137 GHQVTAKLLVPS-DQIGCVIGKGGQIVQNIRSETG 170 (546)
Q Consensus 137 ~~~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tg 170 (546)
.-.+..++++|. ++...||||+|..|++|-.+.+
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 345678888995 5788999999999999977654
No 168
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=31.32 E-value=1.2e+02 Score=31.08 Aligned_cols=12 Identities=33% Similarity=0.570 Sum_probs=7.3
Q ss_pred CCCCCCCCCCCC
Q 009012 474 NYESRDSKRHGR 485 (546)
Q Consensus 474 ~y~~~~~~~~g~ 485 (546)
+|++|...|.|+
T Consensus 365 ~~gGrGgGRGgg 376 (465)
T KOG3973|consen 365 NWGGRGGGRGGG 376 (465)
T ss_pred CCCCCCCCCCCC
Confidence 677777655543
No 169
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=30.31 E-value=1.5e+02 Score=30.42 Aligned_cols=11 Identities=27% Similarity=0.235 Sum_probs=5.4
Q ss_pred HHHhcCceEEE
Q 009012 395 MRRLTKANIRI 405 (546)
Q Consensus 395 I~~~tga~I~i 405 (546)
+|+.|-++|+-
T Consensus 286 ~Re~Taski~k 296 (465)
T KOG3973|consen 286 RRERTASKIHK 296 (465)
T ss_pred hhhhhhhhhcc
Confidence 34555555543
No 170
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=25.11 E-value=1.1e+02 Score=25.83 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=24.1
Q ss_pred ceEEEEcCHHHHHHHHHHHHHHHHhcc
Q 009012 420 EMVQISGDLDLAKDALIQVMTRLRANL 446 (546)
Q Consensus 420 r~v~I~G~~~~v~~A~~~I~~~l~~~~ 446 (546)
..+.|+|+..+|+.|+..+.+.+++..
T Consensus 75 GslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 75 GALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred eeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 368999999999999999999998753
No 171
>PRK04972 putative transporter; Provisional
Probab=24.69 E-value=9.6e+02 Score=26.69 Aligned_cols=64 Identities=23% Similarity=0.408 Sum_probs=35.9
Q ss_pred eEEEEEeeCCceeEEeccCchHHHHHHh-hcCceEEEecC--CCCCc---ccCCCCceEEEEcCHHHHHHHHHHHH
Q 009012 140 VTAKLLVPSDQIGCVIGKGGQIVQNIRS-ETGAQIRILKD--EHLPS---CALRSDELVQISGEASVVKKALCQIA 209 (546)
Q Consensus 140 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~-~tga~I~i~~~--~~~p~---~~~~~dr~v~I~G~~~~V~~A~~~I~ 209 (546)
....+++|+ ..++|| +++++.- ++|+.|.-... .+++. .....-.++.+.|+++++++..+.+-
T Consensus 303 ~~E~vVv~~---s~liGk---TL~eL~~r~~gv~Vl~I~R~g~~~~~~~~~~L~~GD~LlVvG~~~~i~~l~~~lG 372 (558)
T PRK04972 303 VTEEIVVKN---HNAVGK---RLSQLKLTDHGCFLNRVIRSQIEMPIDDNVVLNKGDVLQVSGDARRVKTIADRIG 372 (558)
T ss_pred EEEEEEEcC---cccCCC---CHHHhCCccCCeEEEEEecCCcccCCCCCCEecCCCEEEEEECHHHHHHHHHHhC
Confidence 344555554 345554 6777742 36776654433 22221 11122346889999999988655543
No 172
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.27 E-value=80 Score=30.34 Aligned_cols=29 Identities=28% Similarity=0.458 Sum_probs=25.0
Q ss_pred EEEEecCCccceEecCCcHHHHHHHHHhC
Q 009012 45 YRYLCPIRKIGSIIGRGGEIVKQLRIDTK 73 (546)
Q Consensus 45 ~rilip~~~vg~IIGk~G~~Ik~I~~~tg 73 (546)
++|.|....-+.|||++|..|++|++.-.
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 66788888889999999999999997654
No 173
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.82 E-value=2.4e+02 Score=25.19 Aligned_cols=43 Identities=35% Similarity=0.423 Sum_probs=34.7
Q ss_pred hHHHHHHhhcCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHh
Q 009012 160 QIVQNIRSETGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLH 213 (546)
Q Consensus 160 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~ 213 (546)
+.++.|.+-.|+-|.+.. ..+|.|.|+.+.|.+|++.|...-+
T Consensus 126 eRlqDi~E~hgvIiE~~E-----------~D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEE-----------YDLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeee-----------ccEEEEeccHHHHHHHHHHHHHHHh
Confidence 466788888888888753 3469999999999999999987643
No 174
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=21.47 E-value=2.2e+02 Score=24.11 Aligned_cols=38 Identities=26% Similarity=0.271 Sum_probs=29.7
Q ss_pred cCceEEEecCCCCCcccCCCCceEEEEcCHHHHHHHHHHHHHHHhcC
Q 009012 169 TGAQIRILKDEHLPSCALRSDELVQISGEASVVKKALCQIASRLHDN 215 (546)
Q Consensus 169 tga~I~i~~~~~~p~~~~~~dr~v~I~G~~~~V~~A~~~I~~~l~~~ 215 (546)
.+++|-+... ....|.|+|+..+|+.|+..|.+.+++.
T Consensus 63 a~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 63 ADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred cCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 3466766542 3446999999999999999999999773
No 175
>PTZ00473 Plasmodium Vir superfamily; Provisional
Probab=21.21 E-value=3.8e+02 Score=28.25 Aligned_cols=10 Identities=40% Similarity=0.507 Sum_probs=5.3
Q ss_pred HHHHHHHHhC
Q 009012 64 IVKQLRIDTK 73 (546)
Q Consensus 64 ~Ik~I~~~tg 73 (546)
+||.|++|+.
T Consensus 10 i~k~lk~ey~ 19 (420)
T PTZ00473 10 IVKALKKEYP 19 (420)
T ss_pred HHHHHHHhch
Confidence 4555555553
No 176
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=21.04 E-value=92 Score=29.93 Aligned_cols=28 Identities=39% Similarity=0.577 Sum_probs=23.4
Q ss_pred EEEEEcCCcceeEEcCCChhHHHHHHhc
Q 009012 372 TRLLVPTSRIGCLIGKGGSIITEMRRLT 399 (546)
Q Consensus 372 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~t 399 (546)
+++.|-...-|.|||++|+.|++|++.-
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 5577777788999999999999998553
No 177
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=20.96 E-value=2.7e+02 Score=22.38 Aligned_cols=62 Identities=18% Similarity=0.127 Sum_probs=43.4
Q ss_pred CCcceeEEcCCChhHHHHHHhcCceEEEecCCCCCCCCCCCCceEEEEcCHHHHHHHHHHHHHHHH
Q 009012 378 TSRIGCLIGKGGSIITEMRRLTKANIRILPKENLPKIASEDDEMVQISGDLDLAKDALIQVMTRLR 443 (546)
Q Consensus 378 ~~~vG~IIGkgG~~Ik~I~~~tga~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 443 (546)
.+.-|.|- |=..+.+|-+..++.++..-+|...- ...+.+++|.|+..++..|-+.++..|.
T Consensus 24 are~gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~v--~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 24 AREDGVLA--GLEEAEEIFEKLGLEVEWLVKDGDRV--EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp ESSSEEE---SHHHHHHHHHHCTEEEEESS-TT-EE--ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred eCCCEEEE--CHHHHHHHHhhccEEEEEEeCCCCCc--cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 33334443 55788899888899998876553221 2456789999999999999888877664
Done!