Query 010746
Match_columns 502
No_of_seqs 312 out of 2036
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 04:05:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010746.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010746hhsearch_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 6.5E-47 1.4E-51 389.4 36.0 398 9-428 9-416 (485)
2 KOG1676 K-homology type RNA bi 100.0 3.3E-44 7.2E-49 362.5 31.4 328 42-422 52-390 (600)
3 KOG2193 IGF-II mRNA-binding pr 100.0 2E-42 4.3E-47 333.2 21.5 353 39-424 194-567 (584)
4 KOG2192 PolyC-binding hnRNP-K 100.0 5.8E-35 1.3E-39 266.6 22.9 343 23-422 28-385 (390)
5 KOG1676 K-homology type RNA bi 100.0 3.2E-29 7E-34 254.0 19.4 229 41-315 136-373 (600)
6 KOG2191 RNA-binding protein NO 100.0 5.6E-27 1.2E-31 220.7 20.8 237 42-300 37-282 (402)
7 KOG2193 IGF-II mRNA-binding pr 99.9 6.3E-28 1.4E-32 233.2 9.0 242 139-424 197-484 (584)
8 KOG2191 RNA-binding protein NO 99.9 5.5E-23 1.2E-27 193.8 23.1 170 139-424 37-207 (402)
9 KOG2192 PolyC-binding hnRNP-K 99.9 6.8E-23 1.5E-27 187.7 14.2 172 260-455 46-217 (390)
10 KOG2190 PolyC-binding proteins 99.8 7.1E-20 1.5E-24 189.4 16.2 160 261-424 42-211 (485)
11 TIGR03665 arCOG04150 arCOG0415 99.6 3.8E-15 8.2E-20 135.3 12.8 146 145-421 2-151 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.6 3.1E-15 6.8E-20 135.8 9.3 137 48-216 2-152 (172)
13 PRK13763 putative RNA-processi 99.6 2.9E-14 6.3E-19 130.3 14.7 65 141-215 3-71 (180)
14 PRK13763 putative RNA-processi 99.6 3.4E-14 7.3E-19 129.9 12.9 141 44-216 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.4 9.7E-13 2.1E-17 99.8 7.5 64 349-416 2-65 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 2.1E-12 4.7E-17 97.9 6.9 64 142-209 1-64 (65)
17 cd02394 vigilin_like_KH K homo 99.3 6.9E-12 1.5E-16 94.2 5.7 61 349-416 2-62 (62)
18 KOG2208 Vigilin [Lipid transpo 99.2 1.8E-11 3.8E-16 134.4 9.2 307 42-422 199-563 (753)
19 cd02393 PNPase_KH Polynucleoti 99.2 3.7E-11 8E-16 89.6 8.0 58 347-415 2-60 (61)
20 KOG2279 Kinase anchor protein 99.2 3.4E-11 7.4E-16 121.9 10.2 231 137-419 64-366 (608)
21 PF00013 KH_1: KH domain syndr 99.2 1E-11 2.2E-16 92.6 4.4 60 348-415 1-60 (60)
22 KOG2279 Kinase anchor protein 99.2 6.1E-11 1.3E-15 120.1 9.7 234 40-303 64-337 (608)
23 cd00105 KH-I K homology RNA-bi 99.2 1.2E-10 2.6E-15 88.0 8.1 62 349-415 2-63 (64)
24 PF00013 KH_1: KH domain syndr 99.2 3.3E-11 7.2E-16 89.9 4.2 60 142-209 1-60 (60)
25 cd02394 vigilin_like_KH K homo 99.1 6.5E-11 1.4E-15 88.9 5.5 60 143-209 2-61 (62)
26 cd02393 PNPase_KH Polynucleoti 99.1 3.4E-10 7.5E-15 84.3 7.8 58 141-209 2-60 (61)
27 KOG2208 Vigilin [Lipid transpo 99.1 4.1E-10 8.9E-15 123.7 9.2 290 42-422 345-636 (753)
28 cd00105 KH-I K homology RNA-bi 99.0 7.1E-10 1.5E-14 83.7 7.5 62 143-209 2-63 (64)
29 PF13014 KH_3: KH domain 99.0 8.7E-10 1.9E-14 76.1 5.3 42 54-95 1-43 (43)
30 PF13014 KH_3: KH domain 98.9 2.9E-09 6.3E-14 73.5 5.4 43 357-403 1-43 (43)
31 smart00322 KH K homology RNA-b 98.9 1.2E-08 2.7E-13 77.5 8.9 66 347-419 3-68 (69)
32 COG1094 Predicted RNA-binding 98.8 7.4E-08 1.6E-12 86.8 13.5 147 42-217 6-166 (194)
33 smart00322 KH K homology RNA-b 98.8 4.6E-08 1E-12 74.3 8.7 66 141-213 3-68 (69)
34 COG1094 Predicted RNA-binding 98.7 1.2E-07 2.5E-12 85.5 11.8 54 356-421 111-164 (194)
35 KOG2113 Predicted RNA binding 98.4 7.4E-07 1.6E-11 84.7 7.6 136 260-412 24-173 (394)
36 cd02395 SF1_like-KH Splicing f 98.3 2.4E-06 5.1E-11 72.5 8.1 67 355-421 14-95 (120)
37 cd02395 SF1_like-KH Splicing f 98.3 3.3E-06 7.2E-11 71.7 8.2 68 149-216 14-96 (120)
38 PRK08406 transcription elongat 98.1 4.7E-06 1E-10 72.8 6.2 103 44-176 32-134 (140)
39 KOG2113 Predicted RNA binding 98.1 5.1E-06 1.1E-10 79.2 6.6 141 139-314 24-164 (394)
40 TIGR02696 pppGpp_PNP guanosine 98.0 2.2E-05 4.8E-10 85.1 9.1 97 107-215 545-642 (719)
41 PRK08406 transcription elongat 97.8 7.4E-05 1.6E-09 65.4 6.8 103 262-382 32-134 (140)
42 TIGR01952 nusA_arch NusA famil 97.6 0.00011 2.4E-09 64.1 5.7 103 45-177 34-136 (141)
43 TIGR03591 polynuc_phos polyrib 97.6 0.00013 2.8E-09 80.5 7.4 97 108-215 518-615 (684)
44 TIGR02696 pppGpp_PNP guanosine 97.6 0.00016 3.4E-09 78.6 7.9 67 344-421 575-642 (719)
45 KOG0119 Splicing factor 1/bran 97.5 0.0006 1.3E-08 69.3 10.4 78 138-215 135-230 (554)
46 KOG0119 Splicing factor 1/bran 97.4 0.00098 2.1E-08 67.9 10.7 75 346-422 137-231 (554)
47 TIGR01952 nusA_arch NusA famil 97.4 0.00028 6.2E-09 61.5 5.7 103 263-383 34-136 (141)
48 PLN00207 polyribonucleotide nu 97.3 0.00029 6.4E-09 78.3 5.7 97 108-215 652-750 (891)
49 KOG0336 ATP-dependent RNA heli 97.3 0.00025 5.5E-09 70.7 4.5 63 33-98 36-98 (629)
50 TIGR03591 polynuc_phos polyrib 97.1 0.00079 1.7E-08 74.3 6.2 66 345-421 549-615 (684)
51 COG0195 NusA Transcription elo 97.0 0.0017 3.8E-08 59.5 6.7 104 45-179 77-180 (190)
52 COG1185 Pnp Polyribonucleotide 97.0 0.0013 2.9E-08 70.1 6.8 97 108-215 519-616 (692)
53 KOG1588 RNA-binding protein Sa 96.8 0.0012 2.7E-08 62.4 4.0 41 40-80 88-134 (259)
54 KOG0336 ATP-dependent RNA heli 96.8 0.0014 3E-08 65.6 4.4 72 136-215 42-113 (629)
55 KOG2814 Transcription coactiva 96.7 0.001 2.2E-08 64.7 3.0 69 43-125 56-124 (345)
56 COG0195 NusA Transcription elo 96.7 0.0038 8.2E-08 57.3 6.4 102 264-384 78-179 (190)
57 KOG2814 Transcription coactiva 96.7 0.0017 3.7E-08 63.2 4.3 72 139-216 55-126 (345)
58 cd02134 NusA_KH NusA_K homolog 96.7 0.0027 5.9E-08 47.1 4.5 37 43-79 24-60 (61)
59 PRK11824 polynucleotide phosph 96.7 0.0017 3.6E-08 72.0 4.5 97 108-215 521-618 (693)
60 KOG1588 RNA-binding protein Sa 96.6 0.0056 1.2E-07 58.1 6.8 44 136-179 87-136 (259)
61 PLN00207 polyribonucleotide nu 96.5 0.0032 7E-08 70.2 5.0 67 344-421 682-750 (891)
62 COG1185 Pnp Polyribonucleotide 96.4 0.0046 9.9E-08 66.1 5.3 69 345-424 550-619 (692)
63 cd02134 NusA_KH NusA_K homolog 96.2 0.009 2E-07 44.3 4.6 36 347-382 25-60 (61)
64 PRK12328 nusA transcription el 96.1 0.023 5.1E-07 57.3 8.3 96 53-180 251-347 (374)
65 PRK04163 exosome complex RNA-b 96.0 0.013 2.9E-07 56.1 6.2 64 348-422 146-210 (235)
66 PRK00468 hypothetical protein; 96.0 0.0067 1.5E-07 46.9 3.3 34 40-73 26-59 (75)
67 TIGR01953 NusA transcription t 96.0 0.02 4.4E-07 57.7 7.4 96 53-179 243-339 (341)
68 TIGR01953 NusA transcription t 95.9 0.017 3.8E-07 58.2 6.8 96 271-385 243-339 (341)
69 PRK12328 nusA transcription el 95.9 0.021 4.5E-07 57.7 7.2 97 271-387 251-348 (374)
70 PRK12327 nusA transcription el 95.8 0.013 2.8E-07 59.5 5.4 96 53-179 245-341 (362)
71 PF14611 SLS: Mitochondrial in 95.7 0.17 3.7E-06 47.6 12.3 131 46-217 28-167 (210)
72 TIGR03319 YmdA_YtgF conserved 95.7 0.023 4.9E-07 60.8 7.0 67 345-421 202-270 (514)
73 PRK00106 hypothetical protein; 95.7 0.025 5.4E-07 60.3 7.1 67 345-421 223-291 (535)
74 PRK02821 hypothetical protein; 95.7 0.01 2.2E-07 46.0 3.1 35 41-75 28-62 (77)
75 PRK12704 phosphodiesterase; Pr 95.6 0.025 5.5E-07 60.5 6.8 66 345-420 208-275 (520)
76 COG5176 MSL5 Splicing factor ( 95.6 0.031 6.7E-07 50.8 6.2 44 136-179 143-192 (269)
77 PRK02821 hypothetical protein; 95.5 0.025 5.5E-07 43.8 4.8 35 137-171 27-61 (77)
78 PRK12329 nusA transcription el 95.5 0.035 7.6E-07 57.1 6.9 96 53-179 277-373 (449)
79 PF14611 SLS: Mitochondrial in 95.4 0.32 7E-06 45.7 13.0 87 115-215 4-90 (210)
80 PRK00468 hypothetical protein; 95.4 0.025 5.5E-07 43.7 4.4 34 136-169 25-58 (75)
81 COG1837 Predicted RNA-binding 95.4 0.016 3.4E-07 44.7 3.1 34 40-73 26-59 (76)
82 PRK12327 nusA transcription el 95.3 0.035 7.5E-07 56.4 6.3 96 271-385 245-341 (362)
83 PRK09202 nusA transcription el 95.3 0.044 9.5E-07 57.7 7.1 95 53-179 245-340 (470)
84 COG5176 MSL5 Splicing factor ( 95.2 0.024 5.3E-07 51.4 4.4 43 40-82 144-192 (269)
85 COG1837 Predicted RNA-binding 95.2 0.035 7.6E-07 42.8 4.6 34 136-169 25-58 (76)
86 PRK01064 hypothetical protein; 95.2 0.023 5E-07 44.2 3.6 33 41-73 27-59 (78)
87 PRK12329 nusA transcription el 95.1 0.035 7.7E-07 57.0 5.6 95 271-384 277-372 (449)
88 PRK04163 exosome complex RNA-b 95.0 0.044 9.6E-07 52.5 5.9 62 143-215 147-209 (235)
89 PRK09202 nusA transcription el 94.8 0.05 1.1E-06 57.3 6.0 94 272-385 246-340 (470)
90 PRK11824 polynucleotide phosph 94.8 0.023 5E-07 63.1 3.6 66 345-421 552-618 (693)
91 KOG1067 Predicted RNA-binding 94.8 0.06 1.3E-06 56.1 6.2 97 108-216 564-661 (760)
92 PRK01064 hypothetical protein; 94.6 0.071 1.5E-06 41.5 4.9 34 136-169 25-58 (78)
93 PRK12704 phosphodiesterase; Pr 94.5 0.13 2.9E-06 55.1 8.4 63 143-215 212-276 (520)
94 PRK00106 hypothetical protein; 94.4 0.16 3.4E-06 54.3 8.5 64 142-215 226-291 (535)
95 TIGR03319 YmdA_YtgF conserved 94.4 0.14 3.1E-06 54.8 8.2 64 142-215 205-270 (514)
96 PF13083 KH_4: KH domain; PDB: 93.5 0.044 9.6E-07 42.2 1.7 36 40-75 25-60 (73)
97 PRK12705 hypothetical protein; 92.9 0.11 2.4E-06 55.1 4.3 64 345-418 196-261 (508)
98 KOG3273 Predicted RNA-binding 91.7 0.37 8E-06 43.8 5.4 57 149-217 177-233 (252)
99 COG5166 Uncharacterized conser 91.1 0.77 1.7E-05 47.7 7.6 204 57-382 393-606 (657)
100 KOG4369 RTK signaling protein 91.0 0.083 1.8E-06 59.3 0.7 69 349-421 1342-1410(2131)
101 PRK12705 hypothetical protein; 90.8 0.43 9.3E-06 50.7 5.8 62 144-215 201-264 (508)
102 cd02409 KH-II KH-II (K homolo 90.8 0.36 7.7E-06 35.9 3.9 35 43-77 24-58 (68)
103 KOG0921 Dosage compensation co 90.6 0.82 1.8E-05 50.8 7.7 21 348-368 1085-1105(1282)
104 cd02410 archeal_CPSF_KH The ar 89.5 2.2 4.8E-05 37.2 8.0 91 61-179 23-114 (145)
105 PF13083 KH_4: KH domain; PDB: 88.9 0.18 4E-06 38.7 1.0 33 139-171 27-59 (73)
106 KOG3273 Predicted RNA-binding 88.7 0.21 4.5E-06 45.3 1.3 55 355-421 177-231 (252)
107 COG5166 Uncharacterized conser 88.5 1.1 2.4E-05 46.6 6.4 157 153-410 392-555 (657)
108 cd02409 KH-II KH-II (K homolo 87.9 0.81 1.8E-05 33.9 4.0 35 140-174 24-58 (68)
109 COG1097 RRP4 RNA-binding prote 87.6 1.2 2.5E-05 42.2 5.5 47 47-99 149-195 (239)
110 KOG3875 Peroxisomal biogenesis 87.6 1.7 3.8E-05 42.3 6.8 22 477-498 78-100 (362)
111 cd02414 jag_KH jag_K homology 87.4 0.53 1.2E-05 36.6 2.8 34 45-78 25-58 (77)
112 COG1855 ATPase (PilT family) [ 87.3 1.1 2.3E-05 46.4 5.5 39 142-180 487-525 (604)
113 KOG3875 Peroxisomal biogenesis 87.2 1 2.2E-05 43.8 5.0 14 479-492 73-86 (362)
114 KOG2874 rRNA processing protei 87.1 1.1 2.3E-05 43.0 5.0 51 153-215 161-211 (356)
115 COG1782 Predicted metal-depend 87.0 2.4 5.1E-05 44.4 7.8 95 58-179 43-137 (637)
116 KOG4369 RTK signaling protein 86.8 0.28 6E-06 55.3 1.1 60 41-100 1337-1397(2131)
117 cd02414 jag_KH jag_K homology 86.6 0.75 1.6E-05 35.7 3.2 33 142-174 25-57 (77)
118 KOG1067 Predicted RNA-binding 86.5 0.95 2.1E-05 47.6 4.7 68 343-422 593-661 (760)
119 PF13184 KH_5: NusA-like KH do 86.0 0.52 1.1E-05 35.8 1.9 37 143-179 5-47 (69)
120 PF13184 KH_5: NusA-like KH do 85.9 0.61 1.3E-05 35.4 2.3 36 349-384 5-46 (69)
121 KOG2874 rRNA processing protei 84.2 2.1 4.5E-05 41.1 5.4 51 359-421 161-211 (356)
122 COG1097 RRP4 RNA-binding prote 83.6 3.2 7E-05 39.3 6.4 47 349-406 148-194 (239)
123 PF07650 KH_2: KH domain syndr 83.2 0.55 1.2E-05 36.5 1.0 35 44-78 25-59 (78)
124 PRK13764 ATPase; Provisional 83.2 1.3 2.8E-05 48.2 4.2 43 347-389 481-523 (602)
125 cd02413 40S_S3_KH K homology R 82.6 0.76 1.6E-05 36.1 1.6 37 44-80 30-66 (81)
126 PRK13764 ATPase; Provisional 82.5 3.1 6.6E-05 45.4 6.7 43 141-183 481-523 (602)
127 COG1855 ATPase (PilT family) [ 82.3 0.83 1.8E-05 47.2 2.1 38 44-81 486-523 (604)
128 PRK06418 transcription elongat 81.2 1.9 4.2E-05 38.7 3.8 36 45-81 62-97 (166)
129 PF07650 KH_2: KH domain syndr 80.9 0.73 1.6E-05 35.8 0.9 33 142-174 26-58 (78)
130 PRK06418 transcription elongat 77.4 3.1 6.6E-05 37.4 3.9 37 142-179 62-98 (166)
131 cd02410 archeal_CPSF_KH The ar 77.3 3.3 7.1E-05 36.1 3.9 38 45-82 77-114 (145)
132 TIGR03675 arCOG00543 arCOG0054 75.4 10 0.00023 41.8 8.2 96 58-180 37-132 (630)
133 cd02413 40S_S3_KH K homology R 75.0 3.6 7.8E-05 32.3 3.3 35 142-176 31-65 (81)
134 cd02412 30S_S3_KH K homology R 73.6 2.8 6.1E-05 34.9 2.5 32 45-76 62-93 (109)
135 COG1782 Predicted metal-depend 70.9 11 0.00024 39.6 6.5 96 153-299 41-136 (637)
136 cd02411 archeal_30S_S3_KH K ho 68.2 5 0.00011 31.8 2.7 28 46-73 40-67 (85)
137 COG0092 RpsC Ribosomal protein 65.3 5 0.00011 37.9 2.5 32 43-74 50-81 (233)
138 cd02412 30S_S3_KH K homology R 64.2 6.2 0.00013 32.9 2.7 30 142-171 62-91 (109)
139 cd02411 archeal_30S_S3_KH K ho 61.4 9.1 0.0002 30.3 3.1 28 143-170 40-67 (85)
140 COG0092 RpsC Ribosomal protein 57.4 9 0.0002 36.2 2.7 30 346-375 50-79 (233)
141 TIGR00436 era GTP-binding prot 52.7 17 0.00036 35.5 4.0 30 140-169 220-250 (270)
142 TIGR00436 era GTP-binding prot 52.0 19 0.0004 35.2 4.2 32 345-376 219-251 (270)
143 PF09869 DUF2096: Uncharacteri 51.3 44 0.00096 29.8 5.8 57 139-213 111-167 (169)
144 TIGR03802 Asp_Ala_antiprt aspa 51.0 3.7E+02 0.0079 29.4 14.7 63 142-210 304-377 (562)
145 COG1159 Era GTPase [General fu 48.4 21 0.00046 35.1 3.8 31 139-169 227-258 (298)
146 cd07055 BMC_like_2 Bacterial M 48.2 42 0.00092 24.7 4.4 40 373-417 20-59 (61)
147 PRK15494 era GTPase Era; Provi 47.2 23 0.00049 36.0 4.0 29 141-169 273-302 (339)
148 PRK15494 era GTPase Era; Provi 44.9 29 0.00062 35.2 4.4 37 346-382 272-317 (339)
149 PRK00089 era GTPase Era; Revie 44.9 26 0.00056 34.5 4.0 29 141-169 226-255 (292)
150 PRK03818 putative transporter; 44.9 2.9E+02 0.0063 30.1 12.3 135 45-209 206-359 (552)
151 TIGR03675 arCOG00543 arCOG0054 44.7 22 0.00049 39.3 3.8 42 43-84 92-133 (630)
152 COG1159 Era GTPase [General fu 44.6 29 0.00064 34.2 4.1 34 343-376 225-259 (298)
153 PRK00089 era GTPase Era; Revie 44.3 28 0.0006 34.3 4.1 38 345-382 224-270 (292)
154 COG1847 Jag Predicted RNA-bind 43.2 16 0.00035 33.9 2.0 38 42-79 89-126 (208)
155 KOG1423 Ras-like GTPase ERA [C 40.2 29 0.00063 34.5 3.3 34 138-171 325-359 (379)
156 CHL00048 rps3 ribosomal protei 39.4 28 0.0006 32.8 3.0 32 43-74 65-96 (214)
157 PRK04191 rps3p 30S ribosomal p 39.2 27 0.00059 32.7 2.9 31 46-76 42-72 (207)
158 COG1847 Jag Predicted RNA-bind 39.1 38 0.00083 31.5 3.7 35 142-176 92-126 (208)
159 TIGR01008 rpsC_E_A ribosomal p 38.6 29 0.00064 32.1 3.0 31 45-75 39-69 (195)
160 COG4010 Uncharacterized protei 38.1 1E+02 0.0022 26.8 5.9 43 161-214 126-168 (170)
161 KOG1423 Ras-like GTPase ERA [C 36.9 35 0.00077 33.9 3.3 34 344-377 325-359 (379)
162 PTZ00084 40S ribosomal protein 35.5 33 0.00072 32.4 2.8 33 45-77 45-77 (220)
163 COG1702 PhoH Phosphate starvat 33.9 97 0.0021 31.3 5.9 51 354-416 22-72 (348)
164 KOG3973 Uncharacterized conser 32.0 1E+02 0.0022 30.9 5.6 19 452-470 366-384 (465)
165 TIGR01008 rpsC_E_A ribosomal p 31.0 51 0.0011 30.5 3.3 29 142-170 39-67 (195)
166 PRK15468 carboxysome structura 29.9 1.4E+02 0.003 24.7 5.1 40 168-216 61-100 (111)
167 KOG3973 Uncharacterized conser 29.5 1.7E+02 0.0037 29.4 6.6 10 204-213 103-112 (465)
168 PRK04191 rps3p 30S ribosomal p 29.2 55 0.0012 30.6 3.2 29 143-171 42-70 (207)
169 PTZ00084 40S ribosomal protein 29.1 53 0.0012 31.0 3.1 30 142-171 45-74 (220)
170 CHL00048 rps3 ribosomal protei 28.9 57 0.0012 30.7 3.3 29 142-170 67-95 (214)
171 COG1702 PhoH Phosphate starvat 26.4 1.3E+02 0.0029 30.3 5.4 53 146-210 20-72 (348)
172 TIGR01009 rpsC_bact ribosomal 23.6 68 0.0015 30.1 2.8 29 46-74 64-92 (211)
173 PF02080 TrkA_C: TrkA-C domain 23.4 1.2E+02 0.0026 22.2 3.7 49 160-208 14-69 (71)
174 KOG2044 5'-3' exonuclease HKE1 21.9 2.4E+02 0.0052 31.8 6.6 7 397-403 755-761 (931)
175 cd07049 BMC_EutL_repeat1 ethan 20.9 2.9E+02 0.0062 22.8 5.4 50 167-216 46-100 (103)
176 PF10369 ALS_ss_C: Small subun 20.5 2.7E+02 0.0059 21.2 5.1 42 366-416 16-57 (75)
177 PF09383 NIL: NIL domain; Int 20.5 2.3E+02 0.005 21.3 4.8 51 160-211 16-68 (76)
178 PRK15468 carboxysome structura 20.1 1.6E+02 0.0034 24.4 3.7 25 398-422 76-100 (111)
179 COG0490 Putative regulatory, l 20.1 2.1E+02 0.0045 25.7 4.8 59 353-416 94-158 (162)
180 PF02749 QRPTase_N: Quinolinat 20.0 2.7E+02 0.0059 21.8 5.2 69 346-420 17-85 (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=6.5e-47 Score=389.42 Aligned_cols=398 Identities=42% Similarity=0.609 Sum_probs=314.9
Q ss_pred CCCccCCCCCcccCCCCCCCCCCCCCcccCCCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCc
Q 010746 9 YGKRTHFQSDAATNGGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDE 88 (502)
Q Consensus 9 ~~kr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~e 88 (502)
..++.........++..+++...+. .+....+...++||||+.+.+|.||||+|.+|++|+++|.++|+|.+..++|+|
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~e 87 (485)
T KOG2190|consen 9 PRPKNSTTSNVGDNGSIKRPSLGDP-VISTGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPE 87 (485)
T ss_pred ccccCCCcccccCCCcccccCCCCC-cccCCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCc
Confidence 3445555566655555555555554 344455566669999999999999999999999999999999999999999999
Q ss_pred cEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCC---Cc---CCCCccEEEEEEeeCCceeeeecCCChH
Q 010746 89 RIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLAD---DE---FGELTLITVRMLVPADQIGCVIGKGGQV 162 (502)
Q Consensus 89 rvv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~---~~---~~~~~~~~~~llVp~~~vg~IIGk~G~~ 162 (502)
|+|+|+|...+ ..++++++|++++++.++......+ ++ +....++++|||||.+++|+||||+|+.
T Consensus 88 RIiti~g~~~~--------~~~~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~ 159 (485)
T KOG2190|consen 88 RIITITGNRVE--------LNLSPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSL 159 (485)
T ss_pred ceEEEeccccc--------ccCCchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHH
Confidence 99999997222 2788899999999999987422111 11 1122268999999999999999999999
Q ss_pred HHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCC---CCccc
Q 010746 163 IQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQS---SGVYL 239 (502)
Q Consensus 163 Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~---gg~~~ 239 (502)
||+|+++|||+|+|.++ ++|. +++|.|+|.|.+++|.+|+..|+.+|++++.+......+ +..|.+ .+...
T Consensus 160 Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~s--t~~y~P~~~~~~~~ 233 (485)
T KOG2190|consen 160 IKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVS--TIPYRPSASQGGPV 233 (485)
T ss_pred HHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCC--cccCCCcccccCcc
Confidence 99999999999999999 8998 578999999999999999999999999976542211111 111211 01111
Q ss_pred cCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCC
Q 010746 240 SAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFED 319 (502)
Q Consensus 240 ~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~ 319 (502)
.+.+......+........+.++.+++.+|...++.|+|+++..|+.|+.++++.|.+.....+ |+++++..+.+++
T Consensus 234 ~~s~~~~~~~~~~~~~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~~~ 310 (485)
T KOG2190|consen 234 LPSTAQTSPDAHPFGGIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENPED 310 (485)
T ss_pred ccccccCCcccccccccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCccc
Confidence 1111111111122333345677888999999999999999999999999999999999988754 9999999999988
Q ss_pred C-chhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceE
Q 010746 320 P-SPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEM 398 (502)
Q Consensus 320 ~-~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~ 398 (502)
. +.++++++..++.+.+....+. ...++.+|+||.+++||||||+|++|.+||+.|||.|+|...++. ...++++
T Consensus 311 ~~s~a~~a~~~~~~~~~~~~~~~~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~---~~~~e~~ 386 (485)
T KOG2190|consen 311 RYSMAQEALLLVQPRISENAGDDL-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV---SGVREAL 386 (485)
T ss_pred ccccchhhhhhccccccccccccc-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc---CCcceeE
Confidence 7 8899999999999988777655 788999999999999999999999999999999999999887653 2468899
Q ss_pred EEEEcCHHHHHHHHHHHHHHHHhchhcccC
Q 010746 399 VQITGSLDVASSALSQVTLRLRANTFEREG 428 (502)
Q Consensus 399 v~I~G~~~~v~~A~~~I~~~l~~~~~~~~~ 428 (502)
++|+|+..+...|+.++..++.......++
T Consensus 387 ~~I~~~~~~~~~~~~~~~~~~~~~~~~~~~ 416 (485)
T KOG2190|consen 387 VQITGMLREDLLAQYLIRARLSAPKSSMGG 416 (485)
T ss_pred EEecchhHHHHhhhhhcccccccCccCCCC
Confidence 999999999999999998888776544333
No 2
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=3.3e-44 Score=362.45 Aligned_cols=328 Identities=23% Similarity=0.375 Sum_probs=254.6
Q ss_pred CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (502)
Q Consensus 42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~ 121 (502)
...+.++.||.+++++||||+|+.|..|..++||+|+|+....+..+|.+.++|.+++++. |+..+..+.
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~----------aK~li~evv 121 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV----------AKQLIGEVV 121 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH----------HHHhhhhhh
Confidence 5667899999999999999999999999999999999988777889999999999999532 333333333
Q ss_pred HHHhhhcccCC--CcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010746 122 DRIVAEDSLAD--DEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199 (502)
Q Consensus 122 ~~i~~~~~~~~--~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~ 199 (502)
++.. ... .+......++.+|+||.+.+|.||||+|++||.|++++||++.+..+..... ..++.+.|+|++
T Consensus 122 ~r~~----~~~~~~~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~---~~~KplritGdp 194 (600)
T KOG1676|consen 122 SRGR----PPGGFPDNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIAT---GADKPLRITGDP 194 (600)
T ss_pred hccC----CCCCccccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCC---CCCCceeecCCH
Confidence 3322 110 1112245679999999999999999999999999999999999999854432 478899999999
Q ss_pred HHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCcccccccc
Q 010746 200 AVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGK 279 (502)
Q Consensus 200 ~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk 279 (502)
+.|+.|..+|.++|.+.... .+..++. +++ ..-...+++|.||...||.||||
T Consensus 195 ~~ve~a~~lV~dil~e~~~~-----------~~g~~~~---------~g~-------~~g~~~~~~V~VPr~~VG~IIGk 247 (600)
T KOG1676|consen 195 DKVEQAKQLVADILREEDDE-----------VPGSGGH---------AGV-------RGGGSATREVKVPRSKVGIIIGK 247 (600)
T ss_pred HHHHHHHHHHHHHHHhcccC-----------CCccccc---------cCc-------CccccceeEEeccccceeeEEec
Confidence 99999999999999963211 0111000 000 11123378999999999999999
Q ss_pred CcccccchhhhcCCeEEecCCCC-CCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC------CCCcee--EEE
Q 010746 280 GGGIIKQIRQESGASIKVDSSGA-EGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE------SGDPVI--TTR 350 (502)
Q Consensus 280 ~G~~Ik~i~~~sga~I~v~~~~~-~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~--~~~ 350 (502)
+|++||+|+.+||++|+|.+++. ...+|++.|.|.. ..++.+.+++..+.+..... ...... ...
T Consensus 248 gGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~lI~eii~~~~~~~~~~~~~G~P~~~~~fy 321 (600)
T KOG1676|consen 248 GGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAELINEIIAEAEAGAGGGMGGGAPGLVAQFY 321 (600)
T ss_pred CchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHHHHHHHHHHHhccCCCCcCCCCccceeeEE
Confidence 99999999999999999998766 5789999988864 23444444433332221111 011222 788
Q ss_pred EEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN 422 (502)
Q Consensus 351 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 422 (502)
|.||.+.||.||||+|++||.|..+|||++.+.+. |+..+..+++|+|+|++.+|+.|..||.+++...
T Consensus 322 ~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~IrG~~~QIdhAk~LIr~kvg~~ 390 (600)
T KOG1676|consen 322 MKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFVIRGDKRQIDHAKQLIRDKVGDI 390 (600)
T ss_pred EeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEEEecCcccchHHHHHHHHHhccc
Confidence 99999999999999999999999999999999764 4455778999999999999999999999999774
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=2e-42 Score=333.24 Aligned_cols=353 Identities=25% Similarity=0.357 Sum_probs=274.3
Q ss_pred CCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHH
Q 010746 39 IGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDAL 117 (502)
Q Consensus 39 ~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al 117 (502)
....+.++|+|||-.++|.||||.|+|||.|.+.|.|+|+|.. +..|..|+.|+|.+++|. +.+|+
T Consensus 194 ~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg-------------~s~Ac 260 (584)
T KOG2193|consen 194 QQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG-------------TSKAC 260 (584)
T ss_pred ccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc-------------hHHHH
Confidence 4467899999999999999999999999999999999999984 456889999999999998 57788
Q ss_pred HHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec
Q 010746 118 FRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG 197 (502)
Q Consensus 118 ~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G 197 (502)
.+|++-+..+... +.....+.++++.++..||+||||.|.+||+|+.+||++|.|++-.++..+ +.||.|++.|
T Consensus 261 ~~ILeimqkEA~~----~k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~y--npERTItVkG 334 (584)
T KOG2193|consen 261 KMILEIMQKEAVD----DKVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLY--NPERTITVKG 334 (584)
T ss_pred HHHHHHHHHhhhc----cchhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhccc--CccceEEecc
Confidence 8888877654421 234467889999999999999999999999999999999999987666553 6799999999
Q ss_pred CHHHHHHHHHHHHHHHhcCCCccccccccCCC---------CccCCCCcc--ccCCCcCCCC-CCCccc--Cccccccce
Q 010746 198 EPAVVRKALVQIASRLHENPSRSQHLLLSSSS---------NIYQSSGVY--LSAPLVGSYG-NYSARR--DEASAREFS 263 (502)
Q Consensus 198 ~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~---------~~~~~gg~~--~~~p~~~~~~-~~~~~~--~~~~~~~~~ 263 (502)
..++|..|..+|..+|++..+.+- ...+.. +.++.+.+. +++|..-+.. .|..|. .....+.-.
T Consensus 335 siEac~~AE~eImkKlre~yEnDl--~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~ 412 (584)
T KOG2193|consen 335 SIEACVQAEAEIMKKLRECYENDL--AAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQ 412 (584)
T ss_pred cHHHHHHHHHHHHHHHHHHHhhhH--HHhhccCCCCcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhh
Confidence 999999999999999999755441 111110 011111110 1112111000 111111 112234557
Q ss_pred EEEeccCCccccccccCcccccchhhhcCCeEEecCCC-CCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC-
Q 010746 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSG-AEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE- 341 (502)
Q Consensus 264 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~-~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~- 341 (502)
++|.||...+|+|||++|.+||.|...+|+.|++..+. .+..+|+|+|+|.. ++.++.|.++..++..+
T Consensus 413 V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp---------eaqfKAQgrifgKikEen 483 (584)
T KOG2193|consen 413 VRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP---------EAQFKAQGRIFGKIKEEN 483 (584)
T ss_pred eeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh---------HHHHhhhhhhhhhhhhhc
Confidence 89999999999999999999999999999999998765 34689999999963 45555555555444332
Q ss_pred ----CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010746 342 ----SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL 417 (502)
Q Consensus 342 ----~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 417 (502)
......++.+.||...+|+||||||.+++||++.|+|.|.|+++ +.|- ..+..+|.|+|..-+.+.|+..|.+
T Consensus 484 f~~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrd-qtpd--End~vivriiGhfyatq~aQrki~~ 560 (584)
T KOG2193|consen 484 FFLPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRD-QTPD--ENDQVIVRIIGHFYATQNAQRKIAH 560 (584)
T ss_pred cCCchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEcccc-CCCC--ccceeeeeeechhhcchHHHHHHHH
Confidence 23456788999999999999999999999999999999999765 4453 4566789999999999999999999
Q ss_pred HHHhchh
Q 010746 418 RLRANTF 424 (502)
Q Consensus 418 ~l~~~~~ 424 (502)
+|.+...
T Consensus 561 iv~qvkq 567 (584)
T KOG2193|consen 561 IVNQVKQ 567 (584)
T ss_pred HHHHHHH
Confidence 9988653
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=5.8e-35 Score=266.56 Aligned_cols=343 Identities=21% Similarity=0.340 Sum_probs=224.7
Q ss_pred CCCCCCCCCCCCcccCCCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCccc
Q 010746 23 GGSKRRNPGDETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNL 102 (502)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~ 102 (502)
+...+|..+|- +..-+....+.++||+.++.+|.||||+|++||+|+.+++|+|.|++. +.+||+++|+.+.+.
T Consensus 28 ~~~gkrp~~d~-~~qa~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~t--- 101 (390)
T KOG2192|consen 28 GEFGKRPAEDM-EEQAFKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIET--- 101 (390)
T ss_pred ccccCCcchhh-HHHHhhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHH---
Confidence 44445555553 333346677999999999999999999999999999999999999988 788999999987443
Q ss_pred ccCCccCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCC
Q 010746 103 FEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL 182 (502)
Q Consensus 103 ~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~ 182 (502)
+-+-|.+|+..+. + .......+.+||||+.+++|.|||++|++||+|++++.|+++|..+
T Consensus 102 ----------i~~ilk~iip~le-e------~f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~--- 161 (390)
T KOG2192|consen 102 ----------IGEILKKIIPTLE-E------GFQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE--- 161 (390)
T ss_pred ----------HHHHHHHHhhhhh-h------CCCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc---
Confidence 2334444444432 1 2245677999999999999999999999999999999999999876
Q ss_pred CcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcccccccc--CCCCccCCCCccccCCCcCCCCCCCcccCccccc
Q 010746 183 PLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLS--SSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAR 260 (502)
Q Consensus 183 p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~--~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~ 260 (502)
.|.+++||+|.|.|.+.+|..+++.|.++|.+.+-+.....+. .....|..||..|++.-.....+...++.....
T Consensus 162 -c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~pikgsa~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgp- 239 (390)
T KOG2192|consen 162 -CCPHSTDRVVLIGGKPKRVVECIKIILDLISESPIKGSAQPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGP- 239 (390)
T ss_pred -cCCCCcceEEEecCCcchHHHHHHHHHHHhhcCCcCCcCCcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCC-
Confidence 5678999999999999999999999999999987665332111 112223344444322110000000000000000
Q ss_pred cceEEEeccCCcccccc---ccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccc--
Q 010746 261 EFSLRLVCPAGNIGGVI---GKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCS-- 335 (502)
Q Consensus 261 ~~~~~i~vp~~~~g~II---Gk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~-- 335 (502)
.-|.......+ |+-|.. +.-.+.|...... ...++. ...-++++..-+..-
T Consensus 240 ------p~~~~sdlmay~r~GrpG~r-------ydg~vdFs~detw----------~saidt-w~~SewqmaYePQgGs~ 295 (390)
T KOG2192|consen 240 ------PPPRGSDLMAYDRRGRPGDR-------YDGMVDFSADETW----------PSAIDT-WSPSEWQMAYEPQGGSG 295 (390)
T ss_pred ------CCCCccccceeccCCCCCcc-------ccccccccccccC----------CCcCCC-cCccccccccCCCCCCC
Confidence 00000111111 122222 1111222221110 000000 001111111111000
Q ss_pred ------c--ccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHH
Q 010746 336 ------E--KTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDV 407 (502)
Q Consensus 336 ------~--~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~ 407 (502)
. ..-.+......|.++.||.++-|.||||+|++|++|++++||.|+|... . .++.+|+++|+||.+|
T Consensus 296 ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidep----l-eGsedrIitItGTqdQ 370 (390)
T KOG2192|consen 296 YDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEP----L-EGSEDRIITITGTQDQ 370 (390)
T ss_pred CCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCc----C-CCCCceEEEEeccHHH
Confidence 0 0011234567899999999999999999999999999999999999542 2 3688999999999999
Q ss_pred HHHHHHHHHHHHHhc
Q 010746 408 ASSALSQVTLRLRAN 422 (502)
Q Consensus 408 v~~A~~~I~~~l~~~ 422 (502)
++.|++|++..++.+
T Consensus 371 IqnAQYLlQn~Vkq~ 385 (390)
T KOG2192|consen 371 IQNAQYLLQNSVKQY 385 (390)
T ss_pred HhhHHHHHHHHHHhh
Confidence 999999999999864
No 5
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=3.2e-29 Score=254.01 Aligned_cols=229 Identities=28% Similarity=0.374 Sum_probs=178.7
Q ss_pred CCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC--CCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHH
Q 010746 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET--VPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF 118 (502)
Q Consensus 41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~--~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~ 118 (502)
...++.+|+||..++|+||||+|+|||+|++.+||++.+-.+ ......+.+.|+|+++.| +.|..
T Consensus 136 ~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp~~v-------------e~a~~ 202 (600)
T KOG1676|consen 136 SVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDPDKV-------------EQAKQ 202 (600)
T ss_pred ccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCHHHH-------------HHHHH
Confidence 567899999999999999999999999999999999987643 222367889999998874 45666
Q ss_pred HHHHHHhhhcccCCC-----cCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010746 119 RVHDRIVAEDSLADD-----EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL 193 (502)
Q Consensus 119 ~i~~~i~~~~~~~~~-----~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v 193 (502)
++++.+.++.-.... ........++++.||.+.||.||||+|++||+|+.+|||+|+|.++ +.| .+.||.+
T Consensus 203 lV~dil~e~~~~~~g~~~~~g~~~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpD-d~p---~speR~~ 278 (600)
T KOG1676|consen 203 LVADILREEDDEVPGSGGHAGVRGGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPD-DDP---SSPERPA 278 (600)
T ss_pred HHHHHHHhcccCCCccccccCcCccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecC-CCC---CCcccee
Confidence 666655432111000 0122334489999999999999999999999999999999999998 445 3789999
Q ss_pred EEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCcc
Q 010746 194 QVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNI 273 (502)
Q Consensus 194 ~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~ 273 (502)
.|.|+.++|..|.++|.++|.+..... .+++-. + .| .....+.|.||+.+|
T Consensus 279 ~IiG~~d~ie~Aa~lI~eii~~~~~~~-------------~~~~~~---------G--~P-----~~~~~fy~~VPa~Kc 329 (600)
T KOG1676|consen 279 QIIGTVDQIEHAAELINEIIAEAEAGA-------------GGGMGG---------G--AP-----GLVAQFYMKVPADKC 329 (600)
T ss_pred eeecCHHHHHHHHHHHHHHHHHHhccC-------------CCCcCC---------C--Cc-----cceeeEEEecccccc
Confidence 999999999999999999998853210 000000 0 00 011178899999999
Q ss_pred ccccccCcccccchhhhcCCeEEecCCC--CCCCCeEEEecCCC
Q 010746 274 GGVIGKGGGIIKQIRQESGASIKVDSSG--AEGDDCIIFISTKE 315 (502)
Q Consensus 274 g~IIGk~G~~Ik~i~~~sga~I~v~~~~--~~~~~~ii~i~g~~ 315 (502)
|+|||++|++||.|..++||++.+.+.. ....+++++|.|.+
T Consensus 330 GLvIGrGGEtIK~in~qSGA~~el~r~~p~~~~~ektf~IrG~~ 373 (600)
T KOG1676|consen 330 GLVIGRGGETIKQINQQSGARCELSRQPPNGNPKEKTFVIRGDK 373 (600)
T ss_pred ccccCCCccchhhhcccCCccccccCCCCCCCccceEEEEecCc
Confidence 9999999999999999999999999872 23578999999875
No 6
>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=5.6e-27 Score=220.66 Aligned_cols=237 Identities=28% Similarity=0.393 Sum_probs=172.3
Q ss_pred CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEec---CCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHH
Q 010746 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS---ETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALF 118 (502)
Q Consensus 42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~---~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~ 118 (502)
+.+.++||||+..+|.||||+|++|.+|+++|||+|+++ +.+|++.||+|.|.|+.|++ ...+.
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 449999999999999999999999999999999999997 45899999999999986542 22334
Q ss_pred HHHHHHhhhcccCCC-cC-----CCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCce
Q 010746 119 RVHDRIVAEDSLADD-EF-----GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDEL 192 (502)
Q Consensus 119 ~i~~~i~~~~~~~~~-~~-----~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~ 192 (502)
.|.++|.+....... .+ .....-.++|+||++..|.||||+|.+||.|+|+++|.|+|++- .|.-....||+
T Consensus 104 fI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPq--kpt~~sLqerv 181 (402)
T KOG2191|consen 104 FIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQ--KPTGISLQERV 181 (402)
T ss_pred HHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEeccc--CCCCccceeEE
Confidence 445555433211111 00 11122358999999999999999999999999999999999943 13333467999
Q ss_pred EEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCc
Q 010746 193 LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGN 272 (502)
Q Consensus 193 v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~ 272 (502)
|++.|++++..+|+.+|.++|.+++.....+..+.. +-.|++.-..|...+|..- . ..........+.++...
T Consensus 182 vt~sge~e~~~~A~~~IL~Ki~eDpqs~scln~sya---~vsGpvaNsnPtGspya~~-~---~~~~astas~~sva~~~ 254 (402)
T KOG2191|consen 182 VTVSGEPEQNMKAVSLILQKIQEDPQSGSCLNISYA---NVSGPVANSNPTGSPYAYQ-A---HVLPASTASTISVAAGL 254 (402)
T ss_pred EEecCCHHHHHHHHHHHHHHhhcCCcccceeccchh---cccCcccccCCCCCCCCCC-C---ccccccchhhccccccc
Confidence 999999999999999999999999887665542211 1112111122222222211 1 11222334456788889
Q ss_pred cccccccCcccccchhhhcCCeEEecCC
Q 010746 273 IGGVIGKGGGIIKQIRQESGASIKVDSS 300 (502)
Q Consensus 273 ~g~IIGk~G~~Ik~i~~~sga~I~v~~~ 300 (502)
.|..-|.++.++-.|-..+|..+.++..
T Consensus 255 iG~a~gaG~~~~a~l~~~~G~l~~itq~ 282 (402)
T KOG2191|consen 255 IGGANGAGGAFGAALSGFTGALIAITQA 282 (402)
T ss_pred cccccccccccceeeecccccceeeccc
Confidence 9999999999999999999998877763
No 7
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.95 E-value=6.3e-28 Score=233.20 Aligned_cols=242 Identities=25% Similarity=0.411 Sum_probs=189.5
Q ss_pred ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010746 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS 218 (502)
Q Consensus 139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~ 218 (502)
....+|+|||..+||.||||.|.+||+|...|.|+|.|...++ ++..|++|+|-++++...+|+++|.+++..+..
T Consensus 197 ~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken----~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~ 272 (584)
T KOG2193|consen 197 KDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKEN----AGAAEKIITVHSTPEGTSKACKMILEIMQKEAV 272 (584)
T ss_pred cCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeeccc----CCcccCceEEecCccchHHHHHHHHHHHHHhhh
Confidence 3568999999999999999999999999999999999998854 357899999999999999999999999988643
Q ss_pred ccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEec
Q 010746 219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD 298 (502)
Q Consensus 219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~ 298 (502)
.. ....++.++++.-+.+||++|||.|.+||+|.++||++|.+.
T Consensus 273 ~~------------------------------------k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 273 DD------------------------------------KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred cc------------------------------------chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 32 234567888999999999999999999999999999999999
Q ss_pred CCCCC---CCCeEEEecCC-CccCCCchhHHH-----------HHhhCCccccc--------------c-cc---C----
Q 010746 299 SSGAE---GDDCIIFISTK-EFFEDPSPTITA-----------ALRLQPRCSEK--------------T-ER---E---- 341 (502)
Q Consensus 299 ~~~~~---~~~~ii~i~g~-~~~~~~~~~~~a-----------~~~~~~~~~~~--------------~-~~---~---- 341 (502)
+-..- ..||+|++.|. +.|..+...+.+ ++.++..+... + .+ .
T Consensus 317 ~lqels~ynpERTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q~~l~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~ 396 (584)
T KOG2193|consen 317 KLQELSLYNPERTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQCHLPPGLNLPALGLFPSSSAVSPPHFPPSPVT 396 (584)
T ss_pred ehhhhcccCccceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhccCCCCcccCccccCCCCcccccCCCCCCCCccc
Confidence 74322 47999999883 111111111111 11122211000 0 00 0
Q ss_pred ---------CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHH
Q 010746 342 ---------SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSAL 412 (502)
Q Consensus 342 ---------~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~ 412 (502)
.....-..+|.||...||.|||++|..||.|.+.+||.|+|.+.+ .| +..+|+|+|+|++++.-+|+
T Consensus 397 ~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE-~p---dvseRMViItGppeaqfKAQ 472 (584)
T KOG2193|consen 397 FASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPE-IP---DVSERMVIITGPPEAQFKAQ 472 (584)
T ss_pred cCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCC-CC---CcceeEEEecCChHHHHhhh
Confidence 011233578999999999999999999999999999999997653 33 57899999999999999999
Q ss_pred HHHHHHHHhchh
Q 010746 413 SQVTLRLRANTF 424 (502)
Q Consensus 413 ~~I~~~l~~~~~ 424 (502)
-.|..+|++..+
T Consensus 473 grifgKikEenf 484 (584)
T KOG2193|consen 473 GRIFGKIKEENF 484 (584)
T ss_pred hhhhhhhhhhcc
Confidence 999999998644
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.91 E-value=5.5e-23 Score=193.80 Aligned_cols=170 Identities=25% Similarity=0.446 Sum_probs=138.0
Q ss_pred ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC-CCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE-HLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217 (502)
Q Consensus 139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~-~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~ 217 (502)
..+.+++|||+..+|.||||+|++|.+|+.+|||+|++++.. .+|. .+||+|.|+|+.+++...+..|.++|++.+
T Consensus 37 ~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPG---TTeRvcli~Gt~eai~av~efI~dKire~p 113 (402)
T KOG2191|consen 37 GQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPG---TTERVCLIQGTVEALNAVHEFIADKIREKP 113 (402)
T ss_pred CceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCC---ccceEEEEeccHHHHHHHHHHHHHHHHHhH
Confidence 348999999999999999999999999999999999999863 4564 899999999999999999999999999853
Q ss_pred CccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEe
Q 010746 218 SRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKV 297 (502)
Q Consensus 218 ~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v 297 (502)
..... ...++-|.
T Consensus 114 ~~~~k----------------------------------------~v~~~~pq--------------------------- 126 (402)
T KOG2191|consen 114 QAVAK----------------------------------------PVDILQPQ--------------------------- 126 (402)
T ss_pred HhhcC----------------------------------------CccccCCC---------------------------
Confidence 21100 00000000
Q ss_pred cCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhC
Q 010746 298 DSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATR 377 (502)
Q Consensus 298 ~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tG 377 (502)
. .+ ..-..++.||..-+|.||||+|.+||.|++++|
T Consensus 127 ---t---~~--------------------------------------r~kqikivvPNstag~iigkggAtiK~~~Eqsg 162 (402)
T KOG2191|consen 127 ---T---PD--------------------------------------RIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSG 162 (402)
T ss_pred ---C---cc--------------------------------------ccceeEEeccCCcccceecCCcchHHHHHHhhC
Confidence 0 00 112367899999999999999999999999999
Q ss_pred CeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhchh
Q 010746 378 ASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRANTF 424 (502)
Q Consensus 378 a~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~~~ 424 (502)
|.|+|.+. .|..-.-.+|+|++.|++|+..+|+.+|+++|.+++.
T Consensus 163 a~iqisPq--kpt~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpq 207 (402)
T KOG2191|consen 163 AWIQISPQ--KPTGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQ 207 (402)
T ss_pred cceEeccc--CCCCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCc
Confidence 99999853 3433456789999999999999999999999999864
No 9
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.89 E-value=6.8e-23 Score=187.70 Aligned_cols=172 Identities=27% Similarity=0.384 Sum_probs=141.6
Q ss_pred ccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccc
Q 010746 260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE 339 (502)
Q Consensus 260 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~ 339 (502)
..+++++++..+.+|+||||+|++||.|+.+++++|.|+++.. .+++.+|++.. ....+-+..+.+++.+.+.
T Consensus 46 ~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~--peri~tisad~-----~ti~~ilk~iip~lee~f~ 118 (390)
T KOG2192|consen 46 SRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSG--PERILTISADI-----ETIGEILKKIIPTLEEGFQ 118 (390)
T ss_pred cceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCC--CceeEEEeccH-----HHHHHHHHHHhhhhhhCCC
Confidence 4578999999999999999999999999999999999998774 68999998743 2233333444444444332
Q ss_pred cCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746 340 RESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL 419 (502)
Q Consensus 340 ~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 419 (502)
....++++|+|+++++|.|||++|++||+||+++.|+++|.-. ++| .+++|+|.|.|.+..|..++..|++.|
T Consensus 119 ---~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p---~stdrv~l~~g~~k~v~~~i~~il~~i 191 (390)
T KOG2192|consen 119 ---LPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCP---HSTDRVVLIGGKPKRVVECIKIILDLI 191 (390)
T ss_pred ---CCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCC---CCcceEEEecCCcchHHHHHHHHHHHh
Confidence 2346899999999999999999999999999999999999865 566 589999999999999999999999999
Q ss_pred HhchhcccCccCCCCCCCcCCCCCCCCCCCCCCCCC
Q 010746 420 RANTFEREGALAAHPPVLPYVPMSLDITDGSKYGNR 455 (502)
Q Consensus 420 ~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~~~~~~~ 455 (502)
.+.++ ++...||+|+.+++.+ .||+.
T Consensus 192 ~e~pi--------kgsa~py~p~fyd~t~--dyggf 217 (390)
T KOG2192|consen 192 SESPI--------KGSAQPYDPNFYDETY--DYGGF 217 (390)
T ss_pred hcCCc--------CCcCCcCCccccCccc--ccCCc
Confidence 99765 6678899998887752 45554
No 10
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.83 E-value=7.1e-20 Score=189.45 Aligned_cols=160 Identities=36% Similarity=0.570 Sum_probs=134.2
Q ss_pred cceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccc-
Q 010746 261 EFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTE- 339 (502)
Q Consensus 261 ~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~- 339 (502)
..++|++|+...+|.||||+|..|++||.++.++|++.....+..+|+++|++...-...+++.+|+.+.+..+...+.
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~~~~~~~~al~ka~~~iv~~~~~ 121 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVELNLSPATDALFKAFDMIVFKLEE 121 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccccCCchHHHHHHHHHHHhhcccc
Confidence 3458999999999999999999999999999999999998888899999999942111236677777777665544322
Q ss_pred ---------cCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHH
Q 010746 340 ---------RESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASS 410 (502)
Q Consensus 340 ---------~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~ 410 (502)
.+.....++.+|+||..++|+||||+|++||+|++.|||+|+|..+ .+|. .++|.|+|.|.+++|.+
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 1112235789999999999999999999999999999999999876 7885 68889999999999999
Q ss_pred HHHHHHHHHHhchh
Q 010746 411 ALSQVTLRLRANTF 424 (502)
Q Consensus 411 A~~~I~~~l~~~~~ 424 (502)
|+.+|..+|.+...
T Consensus 198 al~~Is~~L~~~~~ 211 (485)
T KOG2190|consen 198 ALVQISSRLLENPP 211 (485)
T ss_pred HHHHHHHHHHhcCC
Confidence 99999999999653
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=99.62 E-value=3.8e-15 Score=135.27 Aligned_cols=146 Identities=21% Similarity=0.322 Sum_probs=105.4
Q ss_pred EEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEE---ecCHHHHHHHHHHHHHHHhcCCCccc
Q 010746 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQV---AGEPAVVRKALVQIASRLHENPSRSQ 221 (502)
Q Consensus 145 llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I---~G~~~~V~~A~~~I~~~l~~~~~~~~ 221 (502)
|.||.+.++.|||++|++|+.|+++|||+|.+..+ +..|.| +++++++.+|..+|..+........
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~----------~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~- 70 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE----------TGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEK- 70 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC----------CceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHH-
Confidence 56899999999999999999999999999999765 246888 8899999999999998765411000
Q ss_pred cccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcC-CeEEecCC
Q 010746 222 HLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESG-ASIKVDSS 300 (502)
Q Consensus 222 ~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sg-a~I~v~~~ 300 (502)
+-.++| +.+. .-+.+.+-
T Consensus 71 ---------------------------------------------------A~~l~g----------d~y~~~Vi~I~~~ 89 (172)
T TIGR03665 71 ---------------------------------------------------ALKLLD----------DDYMLEVIDLKEY 89 (172)
T ss_pred ---------------------------------------------------HHHhcC----------CcceEEEEEhhhc
Confidence 000000 0000 00011100
Q ss_pred CCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeE
Q 010746 301 GAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASI 380 (502)
Q Consensus 301 ~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I 380 (502)
+.. + + .+ ...+|.|||++|++++.|++.|||+|
T Consensus 90 -----------~~~-------~--~--------------------~~-------~~~~griIG~~G~t~~~ie~~t~~~i 122 (172)
T TIGR03665 90 -----------GKS-------P--N--------------------AL-------RRIKGRIIGEGGKTRRIIEELTGVSI 122 (172)
T ss_pred -----------cCC-------H--H--------------------HH-------HHHHhhhcCCCcHHHHHHHHHHCCeE
Confidence 000 0 0 00 23589999999999999999999999
Q ss_pred EEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746 381 RILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (502)
Q Consensus 381 ~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 421 (502)
.|.. ..|.|+|++++++.|..+|.++++.
T Consensus 123 ~i~~------------~~v~i~G~~~~~~~A~~~i~~li~~ 151 (172)
T TIGR03665 123 SVYG------------KTVGIIGDPEQVQIAREAIEMLIEG 151 (172)
T ss_pred EEcC------------CEEEEECCHHHHHHHHHHHHHHHcC
Confidence 9952 3799999999999999999998855
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=99.60 E-value=3.1e-15 Score=135.81 Aligned_cols=137 Identities=21% Similarity=0.216 Sum_probs=96.7
Q ss_pred EEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEE---cCCCCcccccCCccCCCHHHHHHHHHHHHH
Q 010746 48 YLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY---SSSEGTNLFEDSGEFVSPAQDALFRVHDRI 124 (502)
Q Consensus 48 i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~---G~~e~~~~~~~~~~~~~~a~~al~~i~~~i 124 (502)
|.||.+.+|.|||++|++|++|+++|+|+|++.+. +..|.|. ++++. +++|...|....
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~-------------i~kA~~~I~~i~ 63 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLA-------------VMKAREVVKAIG 63 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHH-------------HHHHHHHHHHHH
Confidence 57899999999999999999999999999999864 4568883 33222 333433333311
Q ss_pred hhhcccCCCc-CCCCccEEEE-EEeeC---------CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceE
Q 010746 125 VAEDSLADDE-FGELTLITVR-MLVPA---------DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELL 193 (502)
Q Consensus 125 ~~~~~~~~~~-~~~~~~~~~~-llVp~---------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v 193 (502)
.. +..++. ......++++ +-|+. ...|+|||++|++++.|++.|+|+|.|.. +.|
T Consensus 64 ~g--f~~e~A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v 129 (172)
T TIGR03665 64 RG--FSPEKALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTV 129 (172)
T ss_pred cC--CCHHHHHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEE
Confidence 11 000000 0001111222 23332 36899999999999999999999999853 469
Q ss_pred EEecCHHHHHHHHHHHHHHHhcC
Q 010746 194 QVAGEPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 194 ~I~G~~~~V~~A~~~I~~~l~~~ 216 (502)
.|.|++++++.|..+|.+++...
T Consensus 130 ~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 130 GIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred EEECCHHHHHHHHHHHHHHHcCC
Confidence 99999999999999999999654
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.59 E-value=2.9e-14 Score=130.33 Aligned_cols=65 Identities=23% Similarity=0.340 Sum_probs=57.5
Q ss_pred EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe----cCHHHHHHHHHHHHHHHhc
Q 010746 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA----GEPAVVRKALVQIASRLHE 215 (502)
Q Consensus 141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~----G~~~~V~~A~~~I~~~l~~ 215 (502)
+...+.||.+.++.|||++|++|+.|+++|||+|.+..+ +..|.|. ++++++.+|+.+|..++..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~----------~g~V~I~~~~~~d~~~i~kA~~~I~ai~~g 71 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE----------TGEVIIEPTDGEDPLAVLKARDIVKAIGRG 71 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC----------CCeEEEEeCCCCCHHHHHHHHHHHHHHhcC
Confidence 367899999999999999999999999999999999755 3568885 8999999999999997763
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.56 E-value=3.4e-14 Score=129.93 Aligned_cols=141 Identities=20% Similarity=0.165 Sum_probs=99.6
Q ss_pred eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEE----cCCCCcccccCCccCCCHHHHHHHH
Q 010746 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIY----SSSEGTNLFEDSGEFVSPAQDALFR 119 (502)
Q Consensus 44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~----G~~e~~~~~~~~~~~~~~a~~al~~ 119 (502)
+...+.||.+.++.|||++|++|+.|+++|||+|++.+. +..|.|. ++++. +.+|...
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 567899999999999999999999999999999999865 4678886 33322 3334433
Q ss_pred HHHHHhhhcccCCCc-CCCCccEEEEE-E----ee-----CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCC
Q 010746 120 VHDRIVAEDSLADDE-FGELTLITVRM-L----VP-----ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALS 188 (502)
Q Consensus 120 i~~~i~~~~~~~~~~-~~~~~~~~~~l-l----Vp-----~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~ 188 (502)
+...+.. +..++. ......+..++ - .+ ...+|+|||++|++++.|++.|||+|.|..+
T Consensus 65 I~ai~~g--f~~e~A~~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~~--------- 133 (180)
T PRK13763 65 VKAIGRG--FSPEKALRLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGK--------- 133 (180)
T ss_pred HHHHhcC--CCHHHHHHHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcCC---------
Confidence 3332211 000000 00011112221 1 11 1368999999999999999999999999533
Q ss_pred CCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746 189 FDELLQVAGEPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 189 ~er~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (502)
.|.|.|++++++.|...|..++...
T Consensus 134 ---~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 134 ---TVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred ---EEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 4999999999999999999999654
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=99.39 E-value=9.7e-13 Score=99.76 Aligned_cols=64 Identities=39% Similarity=0.605 Sum_probs=57.4
Q ss_pred EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010746 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT 416 (502)
Q Consensus 349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 416 (502)
.+|.||.+.+|+|||++|++|++|+++|||+|++.+... + ...+|.|+|.|++++|..|+.||.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~-~---~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL-P---GSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC-C---CCCceEEEEEeCHHHHHHHHHhhC
Confidence 689999999999999999999999999999999976532 2 467899999999999999999873
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=99.35 E-value=2.1e-12 Score=97.86 Aligned_cols=64 Identities=47% Similarity=0.783 Sum_probs=57.9
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 209 (502)
+++|+||.+.+++|||++|.+|++|+++|||+|.+.+... + ...+|+|+|+|++++|.+|+.+|
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 3789999999999999999999999999999999987632 2 36789999999999999999887
No 17
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.27 E-value=6.9e-12 Score=94.24 Aligned_cols=61 Identities=20% Similarity=0.335 Sum_probs=54.8
Q ss_pred EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010746 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT 416 (502)
Q Consensus 349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 416 (502)
.+|.||.+++++|||++|++|++|+++|||+|.+++.. +.++.|+|+|++++|..|+.+|+
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 57899999999999999999999999999999997542 45679999999999999988873
No 18
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.24 E-value=1.8e-11 Score=134.36 Aligned_cols=307 Identities=22% Similarity=0.271 Sum_probs=197.7
Q ss_pred CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (502)
Q Consensus 42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~ 121 (502)
.-+..++.+-...+.++||++|.+++.++.++.+.|+|+... .......|.+...++..+ ..-.++++.++-
T Consensus 199 r~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn--~~~~~~~i~~~~~~~~~~------~~~i~~~~~~le 270 (753)
T KOG2208|consen 199 RSVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSN--KSSPSNKIDGRLNSSSSI------NVEIQEALTRLE 270 (753)
T ss_pred eeEEEEeeccccchhhhccccccccccccccceeEEEccccc--ccchhhhhccccccceeh------hhhhHHHHHHhc
Confidence 347788999999999999999999999999999999998652 222334444433332110 000111111110
Q ss_pred H-----HHhhhccc-------------------------CC-------------Cc--------------CCCCccEEEE
Q 010746 122 D-----RIVAEDSL-------------------------AD-------------DE--------------FGELTLITVR 144 (502)
Q Consensus 122 ~-----~i~~~~~~-------------------------~~-------------~~--------------~~~~~~~~~~ 144 (502)
. .+....+. .+ +. .-....+.+.
T Consensus 271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~ 350 (753)
T KOG2208|consen 271 SEFDYDEIIYRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIK 350 (753)
T ss_pred ChhhhhhhhhccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeE
Confidence 0 00000000 00 00 0112235677
Q ss_pred EEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCcccccc
Q 010746 145 MLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLL 224 (502)
Q Consensus 145 llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~ 224 (502)
+-+-...+..++||+|.+|.+|++++.|.|.+... .+.+..+.++|...++.+|...|...+.+...
T Consensus 351 ~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~-------~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n------ 417 (753)
T KOG2208|consen 351 REIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ-------GSNNKKVVITGVSANDEKAVEDVEKIIAEILN------ 417 (753)
T ss_pred EeecHHhhhhhcCCCCccHHHHHHhhhhceecccc-------cCCCCCeEEeccccchhHHHHHHHHHHHhhhc------
Confidence 88889999999999999999999999999999763 25677899999999999999999998877421
Q ss_pred ccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcC-CeEEecCCCCC
Q 010746 225 LSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESG-ASIKVDSSGAE 303 (502)
Q Consensus 225 ~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sg-a~I~v~~~~~~ 303 (502)
......+.+|...+.++||.+|..|+.|..+++ +.|++......
T Consensus 418 -----------------------------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~~~ 462 (753)
T KOG2208|consen 418 -----------------------------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNNNS 462 (753)
T ss_pred -----------------------------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCCcc
Confidence 023456889999999999999999999999999 88888875543
Q ss_pred CCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEe
Q 010746 304 GDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL 383 (502)
Q Consensus 304 ~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 383 (502)
...-.+...... ++. .+..++.+.... .........+...+.|..+.+..+|+.|..+ +..+...-++
T Consensus 463 ~~~~~~~~~~~d-v~~---~~~~~~~~~~~a----~~~~~~~~~~~d~~~~~~~~~~~~g~~~~i~----d~~~~~~i~~ 530 (753)
T KOG2208|consen 463 SDMVTIRGISKD-VEK---SVSLLKALKADA----KNLKFRDVVTKDKLLPVKYIGKEIGKNGTIR----DSLGDKSIFP 530 (753)
T ss_pred cccceEeccccc-cch---hHHHHHhhhhhh----hcchhhhhhhccccchHHhhcccccCceeee----ccCCceeecc
Confidence 222222211111 111 111111111000 0001112345666777778777777766655 4555555554
Q ss_pred cCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746 384 TNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN 422 (502)
Q Consensus 384 ~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 422 (502)
... ..++..++|.|..+.|..|.+.+..++...
T Consensus 531 ~~~------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~~ 563 (753)
T KOG2208|consen 531 PNE------DEDHEKITIEGKLELVLEAPAELKALIEAL 563 (753)
T ss_pred ccc------ccccceeeecccccchhhhHHHHHhcchhh
Confidence 331 356678999999999999999888777663
No 19
>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=99.23 E-value=3.7e-11 Score=89.57 Aligned_cols=58 Identities=26% Similarity=0.354 Sum_probs=52.5
Q ss_pred eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHH
Q 010746 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQV 415 (502)
Q Consensus 347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I 415 (502)
....+.||.+++|+|||++|++|++|+++|||+|.|.. ++.|.|+|+ +++++.|+.+|
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 45789999999999999999999999999999999953 347999998 99999999887
No 20
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.23 E-value=3.4e-11 Score=121.91 Aligned_cols=231 Identities=26% Similarity=0.385 Sum_probs=168.1
Q ss_pred CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746 137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (502)
....+.+++.||...|.+++|+.|.+|+.|+..++++|.+..++ . ..++..++.|.+.+|.+|...+..++.++
T Consensus 64 ~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed-~-----g~e~~~~~~~~p~~v~~a~a~~~~~~~~~ 137 (608)
T KOG2279|consen 64 PQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTED-V-----GDERVLLISGFPVQVCKAKAAIHQILTEN 137 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-C-----CcccchhhccCCCCCChHHHHHHHHHhcC
Confidence 44678899999999999999999999999999999999998773 2 34666777779999999999999999774
Q ss_pred CCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEE
Q 010746 217 PSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIK 296 (502)
Q Consensus 217 ~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~ 296 (502)
. .+.....+|...++.|+|++|++++.++..++++|.
T Consensus 138 ~-------------------------------------------pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~ 174 (608)
T KOG2279|consen 138 T-------------------------------------------PVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKIT 174 (608)
T ss_pred C-------------------------------------------cccccccchhhhcccccccchhhhcchhcccccccc
Confidence 2 345567789999999999999999999999999999
Q ss_pred ecCCCCCCCCeEEEecCCCccCCC-c-------hhHHHHHhhCC-----cc---------cccc----------------
Q 010746 297 VDSSGAEGDDCIIFISTKEFFEDP-S-------PTITAALRLQP-----RC---------SEKT---------------- 338 (502)
Q Consensus 297 v~~~~~~~~~~ii~i~g~~~~~~~-~-------~~~~a~~~~~~-----~~---------~~~~---------------- 338 (502)
+..+......+++.|.+....... . ..-+...+..+ +. .+.+
T Consensus 175 ~d~ngr~g~~~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~~~~m~~~~~s~~~h~~~~t~ 254 (608)
T KOG2279|consen 175 CDKNGRLGLSRLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVRREDMTEPGGAGEPHLWKNTS 254 (608)
T ss_pred cccccccccccceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCccccchhhcccccCCccccCccch
Confidence 998876666777777764422211 0 00000000000 00 0000
Q ss_pred -----c-----cCC-----------------------CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746 339 -----E-----RES-----------------------GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (502)
Q Consensus 339 -----~-----~~~-----------------------~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 385 (502)
+ .+. .....--.|.||..++|.+||+.|++|+.+...|++.+.|..
T Consensus 255 ~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t- 333 (608)
T KOG2279|consen 255 SSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWT- 333 (608)
T ss_pred hccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEe-
Confidence 0 000 111223578999999999999999999999999999988853
Q ss_pred CCCCCCCCC-CceEEEEEcCHHHHHHHHHHHHHHH
Q 010746 386 ENVPKVAYE-DEEMVQITGSLDVASSALSQVTLRL 419 (502)
Q Consensus 386 ~~~P~~~~~-~~r~v~I~G~~~~v~~A~~~I~~~l 419 (502)
.|..... .-.++.+.|+..-+..|+.|+..+.
T Consensus 334 --~pyt~~v~~~qic~~egkqh~~n~vl~ml~~~~ 366 (608)
T KOG2279|consen 334 --QPYTSRVLQLQICVNEGKQHYENSVLEMLTVHV 366 (608)
T ss_pred --ccccchhhhhhhheecchhHHHHHHHhhhhccC
Confidence 2321000 1146789999999999999888433
No 21
>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=99.22 E-value=1e-11 Score=92.60 Aligned_cols=60 Identities=33% Similarity=0.530 Sum_probs=54.1
Q ss_pred EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010746 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV 415 (502)
Q Consensus 348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 415 (502)
|.+|.||.+++|+|||++|++|++|+++|||+|+++++ + ....|+|+|++++|+.|+.+|
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 2 345999999999999999886
No 22
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.19 E-value=6.1e-11 Score=120.08 Aligned_cols=234 Identities=23% Similarity=0.309 Sum_probs=159.9
Q ss_pred CCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHH
Q 010746 40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFR 119 (502)
Q Consensus 40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~ 119 (502)
..+++..++.||...+..+|||.|++|+.|+..|+++|.+.... -.++++.++.|-+. .+++|..++
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-VGDERVLLISGFPV----------QVCKAKAAI-- 130 (608)
T ss_pred chhheeeeEeecccceeeeeccccCCcchhhcccccceecCccc-CCcccchhhccCCC----------CCChHHHHH--
Confidence 34789999999999999999999999999999999999997652 23356666665433 345455444
Q ss_pred HHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCH
Q 010746 120 VHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEP 199 (502)
Q Consensus 120 i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~ 199 (502)
++++. .+..+...+-+|...++.|+|++|+++++|+..++|+|.+.... .| ...++..|.+..
T Consensus 131 -~~~~~-----------~~~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~ng---r~--g~~~~~~i~~qq 193 (608)
T KOG2279|consen 131 -HQILT-----------ENTPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKNG---RL--GLSRLIKISGQQ 193 (608)
T ss_pred -HHHHh-----------cCCcccccccchhhhcccccccchhhhcchhccccccccccccc---cc--ccccceeccccc
Confidence 33332 33456778999999999999999999999999999999997651 12 557888999998
Q ss_pred HHHHHHHHHHHHHHhcCCCc-------cc-cccccCCCCc-----cCCCCcc----------ccCCCcCC----------
Q 010746 200 AVVRKALVQIASRLHENPSR-------SQ-HLLLSSSSNI-----YQSSGVY----------LSAPLVGS---------- 246 (502)
Q Consensus 200 ~~V~~A~~~I~~~l~~~~~~-------~~-~~~~~~~~~~-----~~~gg~~----------~~~p~~~~---------- 246 (502)
.-++.|..++.+.+.++-+. .+ ...+-.+.+. +.+++.. +..|....
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 88999999998888775221 11 0111111111 1111100 01111000
Q ss_pred ----CCCCCcccC---ccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCC
Q 010746 247 ----YGNYSARRD---EASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAE 303 (502)
Q Consensus 247 ----~~~~~~~~~---~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~ 303 (502)
-+.+..+.+ ..........|.+|...+|.+||..|+.++.+...+++.+.|......
T Consensus 274 ~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~pyt 337 (608)
T KOG2279|consen 274 VVSKEGSWEKPSDDSFQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPYT 337 (608)
T ss_pred EEecccccCCccccccccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEecccc
Confidence 001111111 122334456889999999999999999999999999999999875543
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=99.17 E-value=1.2e-10 Score=87.97 Aligned_cols=62 Identities=37% Similarity=0.627 Sum_probs=55.5
Q ss_pred EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHH
Q 010746 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQV 415 (502)
Q Consensus 349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I 415 (502)
.+|.||.+++++|||++|++|++|+++|||+|.|+.... .+.++.|+|.|+.+++..|+.+|
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 578999999999999999999999999999999975422 35678999999999999998876
No 24
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.15 E-value=3.3e-11 Score=89.86 Aligned_cols=60 Identities=37% Similarity=0.573 Sum_probs=54.1
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 209 (502)
|.+|.||.+++++|||++|.+|++|+++|||+|.|+++ ..+..|+|+|++++|.+|+++|
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 67899999999999999999999999999999999655 1234899999999999999876
No 25
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.14 E-value=6.5e-11 Score=88.90 Aligned_cols=60 Identities=28% Similarity=0.369 Sum_probs=54.7
Q ss_pred EEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (502)
Q Consensus 143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 209 (502)
.+|.||..++++|||++|++|++|+++|||+|.|++.. +.++.|+|+|+.++|..|+.+|
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 57899999999999999999999999999999997752 4578899999999999999876
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=99.10 E-value=3.4e-10 Score=84.33 Aligned_cols=58 Identities=34% Similarity=0.437 Sum_probs=52.3
Q ss_pred EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHH
Q 010746 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQI 209 (502)
Q Consensus 141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I 209 (502)
....|.||.+++++||||+|++|++|+++|||+|.+.+ ++.|.|.|+ +++|++|+.+|
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 35679999999999999999999999999999999854 357999998 99999999876
No 27
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.05 E-value=4.1e-10 Score=123.70 Aligned_cols=290 Identities=17% Similarity=0.200 Sum_probs=189.8
Q ss_pred CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (502)
Q Consensus 42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~ 121 (502)
......+-+-...+..|+||+|.+|.+|++++.|.|.++.. +..+..+++++...++. +|.+.+..+.
T Consensus 345 nn~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~~~----------ka~~~v~~~~ 412 (753)
T KOG2208|consen 345 NNENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSANDE----------KAVEDVEKII 412 (753)
T ss_pred cceeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccchh----------HHHHHHHHHH
Confidence 34667777888999999999999999999999999999985 56788899999988743 2455554444
Q ss_pred HHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcC-ceEEEeecCCCCcccCCCCceEEEecCHH
Q 010746 122 DRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR-AQIRILKDEHLPLCALSFDELLQVAGEPA 200 (502)
Q Consensus 122 ~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg-a~I~i~~~~~~p~~~~~~er~v~I~G~~~ 200 (502)
..+.. ..+...+++|...+.+|||.+|..|+.|.++++ +.|++.... +....+++.|...
T Consensus 413 ~ei~n------------~~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~~~-------~~~~~~~~~~~~~ 473 (753)
T KOG2208|consen 413 AEILN------------SIVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQNNN-------NSSDMVTIRGISK 473 (753)
T ss_pred Hhhhc------------ccccceeecCccchhhhhccccccHHHHHhhcCcEEEecCCCC-------cccccceEecccc
Confidence 44321 134566999999999999999999999999999 666654442 3344588888888
Q ss_pred HHHHHHHHHHHHHhcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccC
Q 010746 201 VVRKALVQIASRLHENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKG 280 (502)
Q Consensus 201 ~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~ 280 (502)
.|..+..++..+........ ......-+...|..+.+..+|+.
T Consensus 474 dv~~~~~~~~~~~~~a~~~~-------------------------------------~~~~~~~d~~~~~~~~~~~~g~~ 516 (753)
T KOG2208|consen 474 DVEKSVSLLKALKADAKNLK-------------------------------------FRDVVTKDKLLPVKYIGKEIGKN 516 (753)
T ss_pred ccchhHHHHHhhhhhhhcch-------------------------------------hhhhhhccccchHHhhcccccCc
Confidence 88887766655544321110 01112234455666666667776
Q ss_pred cccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCc-ee
Q 010746 281 GGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQ-IG 359 (502)
Q Consensus 281 G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~-vg 359 (502)
+..+..+.++..+.+..+. +...+++-+...... .+..+...+.+.+ .......+.+|..+ .-
T Consensus 517 ~~i~d~~~~~~i~~~~~~~-----~~~~i~i~gk~~~v~--~a~~~L~~~~~~~---------~~~~~~~v~~~~~~~~~ 580 (753)
T KOG2208|consen 517 GTIRDSLGDKSIFPPNEDE-----DHEKITIEGKLELVL--EAPAELKALIEAL---------IKATLLEVNNPPGQHRP 580 (753)
T ss_pred eeeeccCCceeeccccccc-----ccceeeecccccchh--hhHHHHHhcchhh---------hhhhhhhccCcchheee
Confidence 6666555555544443333 556667766542111 1111111111111 11233445555444 46
Q ss_pred eeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746 360 CLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRAN 422 (502)
Q Consensus 360 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~~ 422 (502)
++++++....+..+...|+.+..++.. .+.+.++|.|..+.++.|...+.+.++..
T Consensus 581 ~l~~~~~~~~~~~e~~~gv~~~fp~~~-------~~~~e~~i~g~~~~v~aa~~~~~~i~~~~ 636 (753)
T KOG2208|consen 581 FLIGKGIENRTYVEVFGGVVVPFPRSP-------TSSDEVSIKGAKDEVKAAKGRLEEIVEYL 636 (753)
T ss_pred eeeccccccccceeecCcccccCCCCC-------CchhhhccchhHHHHHHhhccchhhhhhc
Confidence 777777777777777777777775542 34447999999999999988888777653
No 28
>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=99.04 E-value=7.1e-10 Score=83.70 Aligned_cols=62 Identities=40% Similarity=0.629 Sum_probs=55.7
Q ss_pred EEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHH
Q 010746 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQI 209 (502)
Q Consensus 143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I 209 (502)
.+|.||.+++++|||++|++|++|+++|+|+|.|..... ...++.|.|.|+.+++..|+.+|
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 579999999999999999999999999999999987522 25688999999999999998876
No 29
>PF13014 KH_3: KH domain
Probab=98.98 E-value=8.7e-10 Score=76.11 Aligned_cols=42 Identities=48% Similarity=0.823 Sum_probs=38.9
Q ss_pred ceeeeecCChhHHHHHHHhhCCeEEecC-CCCCCCccEEEEEc
Q 010746 54 KIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYS 95 (502)
Q Consensus 54 ~~g~iIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G 95 (502)
++|+||||+|++|++|+++|+|+|+|++ ..++..+|+|+|+|
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 4899999999999999999999999998 56788899999987
No 30
>PF13014 KH_3: KH domain
Probab=98.90 E-value=2.9e-09 Score=73.49 Aligned_cols=43 Identities=47% Similarity=0.734 Sum_probs=37.4
Q ss_pred ceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc
Q 010746 357 QIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG 403 (502)
Q Consensus 357 ~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G 403 (502)
+||+|||++|++|++|+++|||+|+|++ +..| .++++.|+|+|
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 5899999999999999999999999987 2333 57889999998
No 31
>smart00322 KH K homology RNA-binding domain.
Probab=98.88 E-value=1.2e-08 Score=77.52 Aligned_cols=66 Identities=29% Similarity=0.538 Sum_probs=58.7
Q ss_pred eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHH
Q 010746 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRL 419 (502)
Q Consensus 347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l 419 (502)
.+.++.||.+.++++||++|++|++|++.||++|.+.... .....|+|.|+.+++..|+.+|.+.+
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 5788999999999999999999999999999999995431 24578999999999999999998876
No 32
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.83 E-value=7.4e-08 Score=86.78 Aligned_cols=147 Identities=22% Similarity=0.266 Sum_probs=101.9
Q ss_pred CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHH
Q 010746 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVH 121 (502)
Q Consensus 42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~ 121 (502)
......+.||.+..+.|||+.|++.+.|.+.++++|.++.. +..|.|........ . -++++..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~~-----~~~V~i~~~~~t~D-------p-----~~~~ka~ 68 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSK-----TGSVTIRTTRKTED-------P-----LALLKAR 68 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEECC-----CCeEEEEecCCCCC-------h-----HHHHHHH
Confidence 44567799999999999999999999999999999999755 68899988632110 0 1122222
Q ss_pred HHHhh--hcccCCCcC-CCCccEEEEE-----Eee------CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746 122 DRIVA--EDSLADDEF-GELTLITVRM-----LVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (502)
Q Consensus 122 ~~i~~--~~~~~~~~~-~~~~~~~~~l-----lVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (502)
+.+.+ ..|..+..- -....+.+.+ ++. ....|+|||++|.+-+.|++-|+|.|.|...
T Consensus 69 d~VkAIgrGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------- 140 (194)
T COG1094 69 DVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYGK-------- 140 (194)
T ss_pred HHHHHHhcCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeCc--------
Confidence 22221 222221100 0000111111 111 1246999999999999999999999999644
Q ss_pred CCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746 188 SFDELLQVAGEPAVVRKALVQIASRLHENP 217 (502)
Q Consensus 188 ~~er~v~I~G~~~~V~~A~~~I~~~l~~~~ 217 (502)
.|.|.|.+++|..|..+|..++...+
T Consensus 141 ----tVaiiG~~~~v~iAr~AVemli~G~~ 166 (194)
T COG1094 141 ----TVAIIGGFEQVEIAREAVEMLINGAP 166 (194)
T ss_pred ----EEEEecChhhhHHHHHHHHHHHcCCC
Confidence 69999999999999999999997643
No 33
>smart00322 KH K homology RNA-binding domain.
Probab=98.76 E-value=4.6e-08 Score=74.30 Aligned_cols=66 Identities=39% Similarity=0.664 Sum_probs=59.1
Q ss_pred EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL 213 (502)
Q Consensus 141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l 213 (502)
++.++.||...+++|||++|.+|++|++.|+++|.+.... .....+.|.|+.+++..|..+|.+.+
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 5788999999999999999999999999999999996541 24678999999999999999998876
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.74 E-value=1.2e-07 Score=85.51 Aligned_cols=54 Identities=22% Similarity=0.314 Sum_probs=48.4
Q ss_pred CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746 356 AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (502)
Q Consensus 356 ~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 421 (502)
...|+|||++|.+-+-|++.|+|.|.|... +|.|.|.+++|+.|...|..++..
T Consensus 111 R~kgRIIG~~GkTr~~IE~lt~~~I~V~g~------------tVaiiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 111 RIKGRIIGREGKTRRAIEELTGVYISVYGK------------TVAIIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred HhhceeeCCCchHHHHHHHHhCCeEEEeCc------------EEEEecChhhhHHHHHHHHHHHcC
Confidence 346899999999999999999999999643 899999999999999999888855
No 35
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.40 E-value=7.4e-07 Score=84.73 Aligned_cols=136 Identities=22% Similarity=0.334 Sum_probs=104.4
Q ss_pred ccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCcccccc-
Q 010746 260 REFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKT- 338 (502)
Q Consensus 260 ~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~- 338 (502)
.+++..+.+|..+++.|+|++|..||.|+.+|...|+-+... .+.++.++|.. +.++.+.+..+...+.+
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~---eePiF~vTg~~------edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRG---EEPIFPVTGRH------EDVRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCC---CCCcceeccCc------hhHHHHhhcCccccceee
Confidence 677888999999999999999999999999999999988755 56888888864 34444444443322221
Q ss_pred ------------ccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010746 339 ------------ERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406 (502)
Q Consensus 339 ------------~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~ 406 (502)
.........+..+.||...+|.|.|.+|.+|+.|++.+...|.-+-++ .+-++.++|.+.
T Consensus 95 l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~~--------~~~Vf~Vtg~~~ 166 (394)
T KOG2113|consen 95 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVRC--------GEPVFCVTGAPK 166 (394)
T ss_pred eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeeccC--------CCceEEEecCCc
Confidence 111123456788899999999999999999999999999998876543 334899999888
Q ss_pred H-HHHHH
Q 010746 407 V-ASSAL 412 (502)
Q Consensus 407 ~-v~~A~ 412 (502)
. +++|.
T Consensus 167 nC~kra~ 173 (394)
T KOG2113|consen 167 NCVKRAR 173 (394)
T ss_pred chhhhcc
Confidence 7 55554
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=98.32 E-value=2.4e-06 Score=72.55 Aligned_cols=67 Identities=21% Similarity=0.328 Sum_probs=51.9
Q ss_pred CCceeeeeCCCchhHHHHHHHhCCeEEEecCCCC-----------CC-CCCCCceEEEEEcC---HHHHHHHHHHHHHHH
Q 010746 355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENV-----------PK-VAYEDEEMVQITGS---LDVASSALSQVTLRL 419 (502)
Q Consensus 355 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~-----------P~-~~~~~~r~v~I~G~---~~~v~~A~~~I~~~l 419 (502)
.+++|.|||++|++||+|+++|||+|.|..+... |. ...++.-.|.|++. .+++..|+.+|..+|
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 4688999999999999999999999999765211 00 01123357899995 599999999999988
Q ss_pred Hh
Q 010746 420 RA 421 (502)
Q Consensus 420 ~~ 421 (502)
..
T Consensus 94 ~~ 95 (120)
T cd02395 94 KP 95 (120)
T ss_pred cc
Confidence 74
No 37
>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=98.28 E-value=3.3e-06 Score=71.65 Aligned_cols=68 Identities=24% Similarity=0.351 Sum_probs=52.2
Q ss_pred CCceeeeecCCChHHHHHHhhcCceEEEeecCCC-----------Cccc-CCCCceEEEecCH---HHHHHHHHHHHHHH
Q 010746 149 ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHL-----------PLCA-LSFDELLQVAGEP---AVVRKALVQIASRL 213 (502)
Q Consensus 149 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~-----------p~~~-~~~er~v~I~G~~---~~V~~A~~~I~~~l 213 (502)
.+.+|.|||++|.+||.|+++|||+|.|..+... |... ...+-.|.|++.. +++.+|+.+|..+|
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 4678999999999999999999999999865211 0000 1123468899964 99999999999999
Q ss_pred hcC
Q 010746 214 HEN 216 (502)
Q Consensus 214 ~~~ 216 (502)
...
T Consensus 94 ~~~ 96 (120)
T cd02395 94 KPA 96 (120)
T ss_pred ccC
Confidence 764
No 38
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=98.13 E-value=4.7e-06 Score=72.85 Aligned_cols=103 Identities=19% Similarity=0.267 Sum_probs=70.1
Q ss_pred eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHH
Q 010746 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDR 123 (502)
Q Consensus 44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~ 123 (502)
-.+.++|+...+|..||++|++|++|++..|-+|.|-+- +- + .++-+..++..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~-----------s~---d-------------~~~fI~n~l~P 84 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY-----------SD---D-------------PEEFIKNIFAP 84 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEc-----------CC---C-------------HHHHHHHHcCC
Confidence 457788899999999999999999999999888876321 11 1 12222222111
Q ss_pred HhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEE
Q 010746 124 IVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176 (502)
Q Consensus 124 i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 176 (502)
..-....- ........+.+.|+....+.+|||+|++|+.++.-++-.+.|
T Consensus 85 a~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 85 AAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 11010000 011223466788999999999999999999999999988766
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=98.12 E-value=5.1e-06 Score=79.17 Aligned_cols=141 Identities=22% Similarity=0.338 Sum_probs=104.2
Q ss_pred ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCC
Q 010746 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPS 218 (502)
Q Consensus 139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~ 218 (502)
..++..+-||..+++.|.|++|.+||.|+.+|.+.|+-+.....| +..++|..+.|+.|++.|...-+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr~eeP--------iF~vTg~~edv~~aRrei~saaeH--- 92 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEP--------IFPVTGRHEDVRRARREIPSAAEH--- 92 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCCCCCC--------cceeccCchhHHHHhhcCccccce---
Confidence 678888999999999999999999999999999999987664434 688999999999999877542211
Q ss_pred ccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEec
Q 010746 219 RSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVD 298 (502)
Q Consensus 219 ~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~ 298 (502)
+.+.-....+ .+...++. ...+....+.+|...++.+.|..|.+|+.+++.++..|.-+
T Consensus 93 ----~~l~~~s~s~-----------Sgg~~~~s------~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~ 151 (394)
T KOG2113|consen 93 ----FGLIRASRSF-----------SGGTNGAS------ASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATP 151 (394)
T ss_pred ----eeeeeecccc-----------cCCCcccc------ccCCCceeeeccceeeeeccccccCccchheecccceEeee
Confidence 1110000000 00001111 23445667888999999999999999999999999999888
Q ss_pred CCCCCCCCeEEEecCC
Q 010746 299 SSGAEGDDCIIFISTK 314 (502)
Q Consensus 299 ~~~~~~~~~ii~i~g~ 314 (502)
-.. .+.++.++|.
T Consensus 152 v~~---~~~Vf~Vtg~ 164 (394)
T KOG2113|consen 152 VRC---GEPVFCVTGA 164 (394)
T ss_pred ccC---CCceEEEecC
Confidence 665 5677777773
No 40
>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=97.98 E-value=2.2e-05 Score=85.14 Aligned_cols=97 Identities=25% Similarity=0.347 Sum_probs=78.0
Q ss_pred ccCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCccc
Q 010746 107 GEFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCA 186 (502)
Q Consensus 107 ~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~ 186 (502)
.+.+..|.++..+|++.+....... .+.....+....+.||.+.++.|||++|.+||.|+++|||+|.|..+
T Consensus 545 ~~aL~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d~------- 616 (719)
T TIGR02696 545 ASALKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIEDD------- 616 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEecC-------
Confidence 3556678888888888766554444 33344556778899999999999999999999999999999999643
Q ss_pred CCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 187 LSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 187 ~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
..|.|.+ +.+.+++|+.+|..++..
T Consensus 617 ----G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 617 ----GTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred ----cEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 4688888 688899999999988874
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.75 E-value=7.4e-05 Score=65.35 Aligned_cols=103 Identities=19% Similarity=0.319 Sum_probs=70.7
Q ss_pred ceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccC
Q 010746 262 FSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERE 341 (502)
Q Consensus 262 ~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~ 341 (502)
-.+.+.|+...+|..||++|++|+.|++..|-+|.+-.-+.+ +..-+..++... -.....-.
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d----------------~~~fI~n~l~Pa--~V~~v~I~ 93 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD----------------PEEFIKNIFAPA--AVRSVTIK 93 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC----------------HHHHHHHHcCCC--EEEEEEEE
Confidence 356778888999999999999999999999888877653311 111222222111 00100000
Q ss_pred CCCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEE
Q 010746 342 SGDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRI 382 (502)
Q Consensus 342 ~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 382 (502)
.........+.|+.+..|..|||+|.+|+.++..++-.+.|
T Consensus 94 ~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 94 KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 01123456678999999999999999999999999988877
No 42
>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=97.61 E-value=0.00011 Score=64.06 Aligned_cols=103 Identities=21% Similarity=0.253 Sum_probs=68.5
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHH
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI 124 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i 124 (502)
.+-++|....+|..||++|++|++|++..|=+|.|-+- +.+++ +-+ .+.+
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVey-----------s~D~~----------------~fI---~N~l 83 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEY-----------SENLE----------------EFV---ANKL 83 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEc-----------CCCHH----------------HHH---HHcC
Confidence 77788999999999999999999998888888876321 11111 000 0000
Q ss_pred hhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEe
Q 010746 125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRIL 177 (502)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~ 177 (502)
.......-..........+.+.||.+..+..|||+|++|+...+-++-++.|.
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 00000000000112234677889999999999999999999999998877663
No 43
>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=97.59 E-value=0.00013 Score=80.45 Aligned_cols=97 Identities=24% Similarity=0.299 Sum_probs=72.3
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (502)
Q Consensus 108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (502)
+.+..|.++..+|++.+.........+.....+....+.||.+.++.|||++|.+||.|+++|||+|.|..+
T Consensus 518 ~al~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~dd-------- 589 (684)
T TIGR03591 518 QALEQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDD-------- 589 (684)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecC--------
Confidence 445556777777777665443332222334456678899999999999999999999999999999999654
Q ss_pred CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 188 SFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 188 ~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
-.|.|.+ ..+.+.+|..+|..+..+
T Consensus 590 ---G~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 590 ---GTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred ---eEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 3577766 577889999998887643
No 44
>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=97.59 E-value=0.00016 Score=78.62 Aligned_cols=67 Identities=22% Similarity=0.275 Sum_probs=59.3
Q ss_pred CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
..+....+.||.+.++.|||.||.+||+|+++|||+|.|.. +..|.|.+ +.+++++|+.+|...+..
T Consensus 575 ~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d-----------~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 575 YAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED-----------DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred CCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec-----------CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 34567899999999999999999999999999999999953 35788888 788999999999998874
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.52 E-value=0.0006 Score=69.33 Aligned_cols=78 Identities=18% Similarity=0.265 Sum_probs=58.3
Q ss_pred CccEEEEEEee------CCceeeeecCCChHHHHHHhhcCceEEEeecCC----------CCc-ccCCCCceEEEec-CH
Q 010746 138 LTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEH----------LPL-CALSFDELLQVAG-EP 199 (502)
Q Consensus 138 ~~~~~~~llVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~----------~p~-~~~~~er~v~I~G-~~ 199 (502)
...++-+|.|| .+.||+|||..|.|.|+|+++|||+|.|.-+.. +.. -....+--|.|+. +-
T Consensus 135 p~~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ 214 (554)
T KOG0119|consen 135 PAKLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQ 214 (554)
T ss_pred ccccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchH
Confidence 33678889998 457899999999999999999999999975210 110 0112233467887 56
Q ss_pred HHHHHHHHHHHHHHhc
Q 010746 200 AVVRKALVQIASRLHE 215 (502)
Q Consensus 200 ~~V~~A~~~I~~~l~~ 215 (502)
|.|++|++.|..+|.+
T Consensus 215 eki~~Ai~vienli~~ 230 (554)
T KOG0119|consen 215 EKIKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 7799999999999986
No 46
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=97.44 E-value=0.00098 Score=67.87 Aligned_cols=75 Identities=17% Similarity=0.321 Sum_probs=58.0
Q ss_pred eeEEEEEecC------CceeeeeCCCchhHHHHHHHhCCeEEEecCCC-------------CCCCCCCCceEEEEEc-CH
Q 010746 346 VITTRILVPS------AQIGCLIGRGGAIISEMRSATRASIRILTNEN-------------VPKVAYEDEEMVQITG-SL 405 (502)
Q Consensus 346 ~~~~~i~VP~------~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~-------------~P~~~~~~~r~v~I~G-~~ 405 (502)
.++.+|.||. ++||.|||..|.|.|.|+++|||+|.|-.+.. .+. ..++--+.|+. |.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~--~~epLH~~Isadt~ 214 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPK--ENEPLHCLISADTQ 214 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccc--cccceeEEEecchH
Confidence 4566777774 58999999999999999999999999976221 111 12333477887 77
Q ss_pred HHHHHHHHHHHHHHHhc
Q 010746 406 DVASSALSQVTLRLRAN 422 (502)
Q Consensus 406 ~~v~~A~~~I~~~l~~~ 422 (502)
|.|++|+++|..+|.+.
T Consensus 215 eki~~Ai~vienli~~a 231 (554)
T KOG0119|consen 215 EKIKKAIAVIENLIQSA 231 (554)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 89999999999999874
No 47
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=97.41 E-value=0.00028 Score=61.49 Aligned_cols=103 Identities=21% Similarity=0.307 Sum_probs=70.4
Q ss_pred eEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCC
Q 010746 263 SLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERES 342 (502)
Q Consensus 263 ~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 342 (502)
.+-+.|....+|..||++|++|+.|++..|-+|.+-.-+.+ +..-+..+ +.+.-...+....
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D----------------~~~fI~N~--l~PA~V~~V~i~~ 95 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN----------------LEEFVANK--LAPAEVKNVTVSE 95 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC----------------HHHHHHHc--CCCceEEEEEEEc
Confidence 56678888999999999999999999888888877653211 11111111 1111111110000
Q ss_pred CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEe
Q 010746 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRIL 383 (502)
Q Consensus 343 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~ 383 (502)
.+......+.||.+..+..|||+|.+|+-..+.++-++.|.
T Consensus 96 ~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 96 FNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred CCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 11235677889999999999999999999999999888773
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.30 E-value=0.00029 Score=78.27 Aligned_cols=97 Identities=16% Similarity=0.242 Sum_probs=76.3
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCce-EEEeecCCCCccc
Q 010746 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQ-IRILKDEHLPLCA 186 (502)
Q Consensus 108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~-I~i~~~~~~p~~~ 186 (502)
+.+..|.++...|++.+.+.......+.....+....|.||.+.++.|||.+|.+||.|.++||+. |.+..+
T Consensus 652 eAL~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~dd------- 724 (891)
T PLN00207 652 RALLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDD------- 724 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCC-------
Confidence 455667778888887776554444333344556788899999999999999999999999999999 877443
Q ss_pred CCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 187 LSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 187 ~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
-.|.|.+ +.+.+.+|+.+|..++.+
T Consensus 725 ----g~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 725 ----GTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred ----eeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 4688888 688899999999988864
No 49
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.30 E-value=0.00025 Score=70.70 Aligned_cols=63 Identities=22% Similarity=0.408 Sum_probs=53.8
Q ss_pred CCcccCCCCCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCC
Q 010746 33 ETEQRGIGSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSE 98 (502)
Q Consensus 33 ~~~~~~~~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e 98 (502)
+++..-...+++++.+.|-++++|.|||++|++|+.|+..|+++|+|-.. ..+-.|+|.|..+
T Consensus 36 ~~~~~aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~---~~e~kv~ifg~~~ 98 (629)
T KOG0336|consen 36 SRDSAAAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC---DLEVKVTIFGINH 98 (629)
T ss_pred CCcccccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc---CceeEEEEechHH
Confidence 44555577889999999999999999999999999999999999999754 3467799999754
No 50
>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=97.08 E-value=0.00079 Score=74.33 Aligned_cols=66 Identities=24% Similarity=0.302 Sum_probs=56.3
Q ss_pred ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
.....++.||.+.++.|||++|++||+|+++|||+|.|.. +..|.|.+ ..+.+++|..+|......
T Consensus 549 ~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------dG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 549 APRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------DGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred CCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------CeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 4567889999999999999999999999999999999953 24677776 678899999998887654
No 51
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=97.01 E-value=0.0017 Score=59.49 Aligned_cols=104 Identities=25% Similarity=0.265 Sum_probs=67.6
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHH
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRI 124 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i 124 (502)
.+-+.+-.+.+|..||++|++|+.|.++.|=+|.|-+-. -+++. -+.+|+. -.
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-----------~d~~~------------fI~nal~----Pa 129 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-----------EDPAE------------FIKNALA----PA 129 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-----------CCHHH------------HHHHhcC----cc
Confidence 344444567789999999999999999998666653221 00000 0111111 00
Q ss_pred hhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 125 VAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
.-....-. ..... .+.+.||.++.+.+|||+|.+++.+.+-||-++.|...
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 00111 67889999999999999999999999999999999765
No 52
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=97.01 E-value=0.0013 Score=70.07 Aligned_cols=97 Identities=24% Similarity=0.270 Sum_probs=73.8
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (502)
Q Consensus 108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (502)
+.+..|.+|-.+|+..+.........+...-.+-...+.|+...+.-+||++|.+|++|.++|||+|.+..
T Consensus 519 ~AL~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--------- 589 (692)
T COG1185 519 KALEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--------- 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC---------
Confidence 34455777777777766554433332333344556778999999999999999999999999999999973
Q ss_pred CCCceEEEecCH-HHHHHHHHHHHHHHhc
Q 010746 188 SFDELLQVAGEP-AVVRKALVQIASRLHE 215 (502)
Q Consensus 188 ~~er~v~I~G~~-~~V~~A~~~I~~~l~~ 215 (502)
+-.|.|.+.. +.+.+|+..|..+..+
T Consensus 590 --dGtv~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 590 --DGTVKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred --CCcEEEEecchHHHHHHHHHHHHHHhh
Confidence 3468898865 7789999999998866
No 53
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.80 E-value=0.0012 Score=62.44 Aligned_cols=41 Identities=29% Similarity=0.476 Sum_probs=35.9
Q ss_pred CCCceEEEEEecCC------ceeeeecCChhHHHHHHHhhCCeEEec
Q 010746 40 GSEDTVYRYLCPLR------KIGSIIGKGGEIVKQLRSETKSNIRIS 80 (502)
Q Consensus 40 ~~~~~~~~i~vp~~------~~g~iIGk~G~~I~~I~~~tga~I~i~ 80 (502)
..-.++.+|+||.+ +||.|+|++|.++|+|+++|+|+|.|-
T Consensus 88 ~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 88 KPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred CceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 34466789999986 799999999999999999999998874
No 54
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.79 E-value=0.0014 Score=65.62 Aligned_cols=72 Identities=22% Similarity=0.365 Sum_probs=59.6
Q ss_pred CCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215 (502)
Q Consensus 136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~ 215 (502)
.....+.+.|-|-+++||.+||++|++|+.||..|+++|+|.+. ..+-.|+|-|...--.+|+..|...+..
T Consensus 42 ag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~--------~~e~kv~ifg~~~m~~kaka~id~~~~k 113 (629)
T KOG0336|consen 42 AGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKC--------DLEVKVTIFGINHMRKKAKASIDRGQDK 113 (629)
T ss_pred cCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEecc--------CceeEEEEechHHHHHHHHhhHhhhhhh
Confidence 34456678889999999999999999999999999999999877 3456799999888777887777655544
No 55
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.74 E-value=0.001 Score=64.74 Aligned_cols=69 Identities=29% Similarity=0.328 Sum_probs=54.2
Q ss_pred ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHH
Q 010746 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHD 122 (502)
Q Consensus 43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~ 122 (502)
+....+++++...+.|||++|.|.++|++||+++|.+|.+ +.....|+|.|-..++ +..|+.+|..
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p--~~n~~~i~i~~~~~~~------------V~~a~~Ri~~ 121 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRP--NTNKEEIKIIGISRNC------------VIQALERIAK 121 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCC--CCCcceEEEeehhHHH------------HHHHHHHHHH
Confidence 5667899999999999999999999999999999999976 4445567777765442 5566666655
Q ss_pred HHh
Q 010746 123 RIV 125 (502)
Q Consensus 123 ~i~ 125 (502)
.|.
T Consensus 122 ~id 124 (345)
T KOG2814|consen 122 LID 124 (345)
T ss_pred HHH
Confidence 553
No 56
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.71 E-value=0.0038 Score=57.30 Aligned_cols=102 Identities=27% Similarity=0.370 Sum_probs=68.2
Q ss_pred EEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCC
Q 010746 264 LRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESG 343 (502)
Q Consensus 264 ~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~ 343 (502)
+...+-.+.+|..||++|.+|+.|.++.|-+|.+-.-+.+ +..-+..++. +.-...+.-...
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d----------------~~~fI~nal~--Pa~v~~V~~~~~ 139 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED----------------PAEFIKNALA--PAEVLSVNIKED 139 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC----------------HHHHHHHhcC--cceEeEEEEEeC
Confidence 3445556778999999999999999999977776643211 1111111111 111111100000
Q ss_pred CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEec
Q 010746 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILT 384 (502)
Q Consensus 344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 384 (502)
+.. ...+.||.+..+.+|||+|.+++-+.+-||-++.|..
T Consensus 140 d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 140 DGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred CCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 112 6788899999999999999999999999999999954
No 57
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.71 E-value=0.0017 Score=63.18 Aligned_cols=72 Identities=24% Similarity=0.333 Sum_probs=59.2
Q ss_pred ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (502)
.....-++|++...++|||++|.+-++|+++|+|+|.++... ...+.++.+.+..++|.+|...|..+|.+.
T Consensus 55 ~~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 55 KDFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred ccchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 345667999999999999999999999999999999997662 133444555558899999999999988775
No 58
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=96.70 E-value=0.0027 Score=47.12 Aligned_cols=37 Identities=30% Similarity=0.433 Sum_probs=34.5
Q ss_pred ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEe
Q 010746 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI 79 (502)
Q Consensus 43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i 79 (502)
.....+.||.+..|..|||+|.+|+.+++.++-+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4688999999999999999999999999999988876
No 59
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=96.67 E-value=0.0017 Score=72.02 Aligned_cols=97 Identities=25% Similarity=0.330 Sum_probs=72.0
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (502)
Q Consensus 108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (502)
+.+..|.++..+|++.+.........+.....+....+.||.+.++.+||++|.+||.|.++||++|.+..
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 45556778888888877654433322223334445667789999999999999999999999999888733
Q ss_pred CCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 188 SFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 188 ~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
+-.|.|.+ ..+.+.+|+.+|..+..+
T Consensus 592 --~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 --DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred --CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 34588888 678889999999887753
No 60
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.59 E-value=0.0056 Score=58.08 Aligned_cols=44 Identities=27% Similarity=0.516 Sum_probs=38.3
Q ss_pred CCCccEEEEEEeeC------CceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 136 GELTLITVRMLVPA------DQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 136 ~~~~~~~~~llVp~------~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
.....++.+++||- +.||+|+|.+|.++|.|+++|+|+|.|--.
T Consensus 87 ~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGr 136 (259)
T KOG1588|consen 87 GKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGR 136 (259)
T ss_pred CCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecC
Confidence 44556788999994 489999999999999999999999999765
No 61
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.46 E-value=0.0032 Score=70.21 Aligned_cols=67 Identities=18% Similarity=0.252 Sum_probs=58.0
Q ss_pred CceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCe-EEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 344 DPVITTRILVPSAQIGCLIGRGGAIISEMRSATRAS-IRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 344 ~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~-I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
.......+.||.+.++.|||.||.+||+|.++||+. |.+. ++-.|.|.+ +.+.++.|+.+|..++.+
T Consensus 682 ~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~-----------ddg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 682 YAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQ-----------DDGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred cCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcC-----------CCeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 356678999999999999999999999999999999 8873 235788888 788999999999988764
No 62
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.37 E-value=0.0046 Score=66.14 Aligned_cols=69 Identities=23% Similarity=0.274 Sum_probs=58.9
Q ss_pred ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCH-HHHHHHHHHHHHHHHhch
Q 010746 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSL-DVASSALSQVTLRLRANT 423 (502)
Q Consensus 345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~-~~v~~A~~~I~~~l~~~~ 423 (502)
.....++.|+.+.+..|||++|.+|++|.++|||+|.|. + +-.|.|.++. +.+..|+..|...+++..
T Consensus 550 aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idie-d----------dGtv~i~~s~~~~~~~ak~~I~~i~~e~e 618 (692)
T COG1185 550 APRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIE-D----------DGTVKIAASDGESAKKAKERIEAITREVE 618 (692)
T ss_pred CCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEec-C----------CCcEEEEecchHHHHHHHHHHHHHHhhcc
Confidence 445678999999999999999999999999999999995 2 2368888855 789999999999998754
Q ss_pred h
Q 010746 424 F 424 (502)
Q Consensus 424 ~ 424 (502)
.
T Consensus 619 v 619 (692)
T COG1185 619 V 619 (692)
T ss_pred c
Confidence 3
No 63
>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=96.20 E-value=0.009 Score=44.32 Aligned_cols=36 Identities=31% Similarity=0.516 Sum_probs=33.4
Q ss_pred eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEE
Q 010746 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRI 382 (502)
Q Consensus 347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i 382 (502)
....+.||.+..|.+|||+|.+|+.+++.++-+|.|
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 64
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.06 E-value=0.023 Score=57.34 Aligned_cols=96 Identities=19% Similarity=0.115 Sum_probs=63.3
Q ss_pred CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (502)
Q Consensus 53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~ 131 (502)
+-+|..||++|+.|+.|.++. |=+|+|-.-.++ + . ..+...+.......
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D-----------~----------------~---~fI~Nal~Pa~V~~ 300 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV-----------P----------------E---IFIARALAPAIISS 300 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC-----------H----------------H---HHHHHhCCCceeeE
Confidence 458999999999999999998 777776321100 0 0 00000000000000
Q ss_pred CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (502)
Q Consensus 132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (502)
-. -....-.+.+.||..+.+..|||+|++++-...-||.+|.|..-+
T Consensus 301 V~--i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~ 347 (374)
T PRK12328 301 VK--IEEEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIG 347 (374)
T ss_pred EE--EcCCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECC
Confidence 00 001123678899999999999999999999999999999998753
No 65
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=96.05 E-value=0.013 Score=56.14 Aligned_cols=64 Identities=17% Similarity=0.260 Sum_probs=52.9
Q ss_pred EEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcC-HHHHHHHHHHHHHHHHhc
Q 010746 348 TTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGS-LDVASSALSQVTLRLRAN 422 (502)
Q Consensus 348 ~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~-~~~v~~A~~~I~~~l~~~ 422 (502)
-..+.||.++++.+||++|.+|+.|.+.|+++|.|-. +-.|.|.++ .+.+..|+.+|...-++.
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~-----------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ-----------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC-----------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 3678899999999999999999999999999999932 347889985 558888888887666554
No 66
>PRK00468 hypothetical protein; Provisional
Probab=96.03 E-value=0.0067 Score=46.86 Aligned_cols=34 Identities=26% Similarity=0.546 Sum_probs=30.2
Q ss_pred CCCceEEEEEecCCceeeeecCChhHHHHHHHhh
Q 010746 40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (502)
Q Consensus 40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~t 73 (502)
.++.+.+++.|..+..|.||||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv 59 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVV 59 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHH
Confidence 3456889999999999999999999999998764
No 67
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.96 E-value=0.02 Score=57.71 Aligned_cols=96 Identities=24% Similarity=0.375 Sum_probs=63.0
Q ss_pred CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (502)
Q Consensus 53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~ 131 (502)
+-+|..||++|+.|+.|.++. |=+|.|-.-. -+++. -+..||.- ..+..-...
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s-----------~d~~~------------fi~nal~P--a~v~~v~i~- 296 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYS-----------DDPAE------------FIANALSP--AKVISVEVL- 296 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcC-----------CCHHH------------HHHHhcCC--ceEEEEEEE-
Confidence 468999999999999999998 7777763211 00000 00011100 000000000
Q ss_pred CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
+ . ..-.+.+.||..+.+..|||+|++++....-||.+|.|...
T Consensus 297 ~---~--~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 297 D---E--DKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred c---C--CCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 0 0 11368899999999999999999999999999999999765
No 68
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.94 E-value=0.017 Score=58.17 Aligned_cols=96 Identities=25% Similarity=0.374 Sum_probs=64.0
Q ss_pred CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349 (502)
Q Consensus 271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 349 (502)
+-+|+.||.+|++|+.|.++. |-+|.+-.-+.+ +..-+..+ +.+.-...+..... .....
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d----------------~~~fi~na--l~Pa~v~~v~i~~~-~~~~~ 303 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDD----------------PAEFIANA--LSPAKVISVEVLDE-DKHSA 303 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--cCCceEEEEEEEcC-CCcEE
Confidence 357999999999999999888 677776543321 00011111 11111111100001 12467
Q ss_pred EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (502)
Q Consensus 350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 385 (502)
.+.||.++.+..|||+|.+++-..+.||.+|.|...
T Consensus 304 ~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 304 EVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred EEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 899999999999999999999999999999999653
No 69
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.92 E-value=0.021 Score=57.72 Aligned_cols=97 Identities=23% Similarity=0.226 Sum_probs=65.3
Q ss_pred CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349 (502)
Q Consensus 271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 349 (502)
+-+|..||.+|.+|+.|.++. |-+|.+-.-+.+ +..-+..+ +.+.-...+... ......
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D----------------~~~fI~Na--l~Pa~V~~V~i~--~~~~~~ 310 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNV----------------PEIFIARA--LAPAIISSVKIE--EEEKKA 310 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--CCCceeeEEEEc--CCCcEE
Confidence 457999999999999999888 677776543311 00111111 111111111111 112467
Q ss_pred EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCC
Q 010746 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNEN 387 (502)
Q Consensus 350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~ 387 (502)
.+.||.++.+..|||+|.+++-..+.||.+|.|..-+.
T Consensus 311 ~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~ 348 (374)
T PRK12328 311 IVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGS 348 (374)
T ss_pred EEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCC
Confidence 88999999999999999999999999999999977543
No 70
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.83 E-value=0.013 Score=59.47 Aligned_cols=96 Identities=23% Similarity=0.285 Sum_probs=63.4
Q ss_pred CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (502)
Q Consensus 53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~ 131 (502)
+-+|..||++|+.|+.|.++. |=+|.|-.- .. + ..+ .+...+.......
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~------------s~--d-------------~~~---fi~nal~Pa~v~~ 294 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDW------------SE--D-------------PAE---FVANALSPAKVVS 294 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEc------------CC--C-------------HHH---HHHHhCCCceEEE
Confidence 468999999999999999998 777776321 10 0 000 0000000000000
Q ss_pred CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
-. ......-.+.+.||..+.+..|||+|.+++-...-||.+|.|...
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 000112367899999999999999999999999999999999776
No 71
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.73 E-value=0.17 Score=47.57 Aligned_cols=131 Identities=14% Similarity=0.135 Sum_probs=87.4
Q ss_pred EEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHh
Q 010746 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIV 125 (502)
Q Consensus 46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~ 125 (502)
+.+.++....-+|...+|..++.|-...||+|.+... +..|.|+|+...++. +...|..++..+.
T Consensus 28 l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k~~~~~----------i~~~i~~~l~~i~ 92 (210)
T PF14611_consen 28 LDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTKSTAEY----------IEASINEILSNIR 92 (210)
T ss_pred eEEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccHHHHHH----------HHHHHHHHHhhcE
Confidence 4455568889999999999999998888999999765 678999998665322 3334444444432
Q ss_pred hhcccCCCcCCCCccEEEEEEeeCCceeeee----cCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEe-----
Q 010746 126 AEDSLADDEFGELTLITVRMLVPADQIGCVI----GKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVA----- 196 (502)
Q Consensus 126 ~~~~~~~~~~~~~~~~~~~llVp~~~vg~II----Gk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~----- 196 (502)
+..+-++.-..-.-. -.....++.|++.|++.|....+ +..+.|.
T Consensus 93 ----------------~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~----------~~~~~i~~~~~~ 146 (210)
T PF14611_consen 93 ----------------TEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPD----------GNKLKISWLASP 146 (210)
T ss_pred ----------------EEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCC----------CCeEEEEEEeec
Confidence 333333322111111 12467889999999999998665 2234444
Q ss_pred cCHHHHHHHHHHHHHHHhcCC
Q 010746 197 GEPAVVRKALVQIASRLHENP 217 (502)
Q Consensus 197 G~~~~V~~A~~~I~~~l~~~~ 217 (502)
-....+..|+..+...+..++
T Consensus 147 ~~~~~~~~a~RlL~~a~~~~~ 167 (210)
T PF14611_consen 147 ENEKRADRAKRLLLWALDYNP 167 (210)
T ss_pred cccchHHHHHHHHHHhccCCc
Confidence 456778889888888775443
No 72
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=95.72 E-value=0.023 Score=60.77 Aligned_cols=67 Identities=19% Similarity=0.243 Sum_probs=52.1
Q ss_pred ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
...+..|.+|. ++-|.||||.|.+|+-+...||++|.|. + +...|+|++ .|---+.|..-|..+|.+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEc---C-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 45667788996 6779999999999999999999999994 2 334788999 776666676666555544
No 73
>PRK00106 hypothetical protein; Provisional
Probab=95.72 E-value=0.025 Score=60.27 Aligned_cols=67 Identities=22% Similarity=0.264 Sum_probs=52.6
Q ss_pred ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
......|.+|. ++-|.||||-|.+|+-+...||++|.|. + +...|+|++ .|---+.|..-|..++.+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---d-------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIID---D-------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEc---C-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 45667888996 6779999999999999999999999994 2 334788999 777666676666555544
No 74
>PRK02821 hypothetical protein; Provisional
Probab=95.72 E-value=0.01 Score=46.05 Aligned_cols=35 Identities=20% Similarity=0.400 Sum_probs=30.8
Q ss_pred CCceEEEEEecCCceeeeecCChhHHHHHHHhhCC
Q 010746 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75 (502)
Q Consensus 41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga 75 (502)
++.+.+.+.|..+.+|.||||+|.+|+.||.--.+
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 45578999999999999999999999999987644
No 75
>PRK12704 phosphodiesterase; Provisional
Probab=95.61 E-value=0.025 Score=60.51 Aligned_cols=66 Identities=20% Similarity=0.235 Sum_probs=50.3
Q ss_pred ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHH
Q 010746 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLR 420 (502)
Q Consensus 345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~ 420 (502)
...+..|.+|. ++-|.||||-|.+|+-+...||++|.|. + +...|.|+| .|-.-+.|..-+...+.
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iid---d-------tp~~v~ls~~~~~rre~a~~~l~~l~~ 275 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIID---D-------TPEAVILSGFDPIRREIARLALEKLVQ 275 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEc---C-------CCCeEEEecCChhhHHHHHHHHHHHHh
Confidence 35567788996 6779999999999999999999999994 2 334888999 66555566555554443
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.61 E-value=0.031 Score=50.80 Aligned_cols=44 Identities=20% Similarity=0.399 Sum_probs=37.2
Q ss_pred CCCccEEEEEEee------CCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 136 GELTLITVRMLVP------ADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 136 ~~~~~~~~~llVp------~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
.....++-++.|| .+.||.|||..|.+.|+|++.|+|+|-|-..
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 3445567778888 5689999999999999999999999999765
No 77
>PRK02821 hypothetical protein; Provisional
Probab=95.53 E-value=0.025 Score=43.82 Aligned_cols=35 Identities=31% Similarity=0.462 Sum_probs=29.6
Q ss_pred CCccEEEEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746 137 ELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (502)
Q Consensus 137 ~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg 171 (502)
....+.++|.+.+.-+|.||||+|.+|+.||.--.
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHH
Confidence 34457899999999999999999999999996533
No 78
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.48 E-value=0.035 Score=57.07 Aligned_cols=96 Identities=20% Similarity=0.226 Sum_probs=62.2
Q ss_pred CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (502)
Q Consensus 53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~ 131 (502)
+-+|..||++|+.|+.|.++. |=+|.|-.-. -++ .+ .|...+.......
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys-----------~Dp----------------~~---fI~NaLsPA~V~~ 326 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWS-----------PDP----------------AT---YIANALSPARVDE 326 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcC-----------CCH----------------HH---HHHHhcCCceeeE
Confidence 468999999999999999998 7777763210 000 00 0000000000000
Q ss_pred CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
-.- .....-.+.+.||..+.+..|||+|++++-...-||.+|.|...
T Consensus 327 V~i-~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s~ 373 (449)
T PRK12329 327 VRL-VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKDS 373 (449)
T ss_pred EEE-EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEeccccH
Confidence 000 00111356899999999999999999999999999999998654
No 79
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=95.43 E-value=0.32 Score=45.71 Aligned_cols=87 Identities=13% Similarity=0.237 Sum_probs=64.4
Q ss_pred HHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEE
Q 010746 115 DALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQ 194 (502)
Q Consensus 115 ~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~ 194 (502)
..+.+|+..+..-...+..+ ... .+.+.++....-.|...+|..++.|-...||+|.+..+ +..|.
T Consensus 4 ~l~~~Il~d~W~l~v~e~v~--~~g--~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~----------~~~i~ 69 (210)
T PF14611_consen 4 KLAERILRDCWNLEVSEEVD--ELG--DLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS----------ENRIR 69 (210)
T ss_pred HHHHHHHHHhcCCcccceee--ccc--eeEEEecchheeeeecCCchHHHHHHHhcCceEEEecC----------CcEEE
Confidence 34556666665443322211 112 33455568889999999999999999999999999766 45799
Q ss_pred EecCHHHHHHHHHHHHHHHhc
Q 010746 195 VAGEPAVVRKALVQIASRLHE 215 (502)
Q Consensus 195 I~G~~~~V~~A~~~I~~~l~~ 215 (502)
|+|+...+..+...|.+++..
T Consensus 70 I~g~k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 70 ITGTKSTAEYIEASINEILSN 90 (210)
T ss_pred EEccHHHHHHHHHHHHHHHhh
Confidence 999999999999999988866
No 80
>PRK00468 hypothetical protein; Provisional
Probab=95.42 E-value=0.025 Score=43.69 Aligned_cols=34 Identities=29% Similarity=0.490 Sum_probs=29.6
Q ss_pred CCCccEEEEEEeeCCceeeeecCCChHHHHHHhh
Q 010746 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
.....+.++|.+..+-+|.||||+|.+|+.||.-
T Consensus 25 ~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 25 EGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred eCCCeEEEEEEEChhhCcceecCCChhHHHHHHH
Confidence 3445688999999999999999999999999964
No 81
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.40 E-value=0.016 Score=44.68 Aligned_cols=34 Identities=21% Similarity=0.444 Sum_probs=30.3
Q ss_pred CCCceEEEEEecCCceeeeecCChhHHHHHHHhh
Q 010746 40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (502)
Q Consensus 40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~t 73 (502)
.+..+.+++.+..+..|.||||+|.+|+.||.-.
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 3567789999999999999999999999998754
No 82
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.32 E-value=0.035 Score=56.41 Aligned_cols=96 Identities=23% Similarity=0.330 Sum_probs=64.2
Q ss_pred CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349 (502)
Q Consensus 271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 349 (502)
+-+|..||.+|.+|+.|.++. |-+|.+-.-+.+ +..-+..+ +.+.-...+... .......
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d----------------~~~fi~na--l~Pa~v~~v~i~-~~~~~~~ 305 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSED----------------PAEFVANA--LSPAKVVSVEVD-DEEEKAA 305 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--CCCceEEEEEEE-cCCCcEE
Confidence 357999999999999999888 677776543321 00011111 111110111000 0112467
Q ss_pred EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (502)
Q Consensus 350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 385 (502)
.+.||.++.+..|||+|.+++--.+.||.+|.|...
T Consensus 306 ~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 306 RVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred EEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 899999999999999999999999999999999754
No 83
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.26 E-value=0.044 Score=57.70 Aligned_cols=95 Identities=20% Similarity=0.264 Sum_probs=62.9
Q ss_pred CceeeeecCChhHHHHHHHhh-CCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccC
Q 010746 53 RKIGSIIGKGGEIVKQLRSET-KSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLA 131 (502)
Q Consensus 53 ~~~g~iIGk~G~~I~~I~~~t-ga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~ 131 (502)
+-+|..||++|+.|+.|.++. |=+|.|-.- .. +. . ..+...+.......
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~------------s~--d~-------------~---~fi~nal~pa~v~~ 294 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILW------------SD--DP-------------A---QFIINALSPAEVSS 294 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEc------------CC--CH-------------H---HHHHHhCCCCEEEE
Confidence 458999999999999999998 777776321 10 00 0 00011110000000
Q ss_pred CCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 132 DDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 132 ~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
-- -....-.+.+.||..+.+..|||+|++|+...+-||.+|.|...
T Consensus 295 v~--~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 295 VV--VDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EE--EeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 00 00011277899999999999999999999999999999999875
No 84
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=95.25 E-value=0.024 Score=51.45 Aligned_cols=43 Identities=23% Similarity=0.400 Sum_probs=36.2
Q ss_pred CCCceEEEEEecC------CceeeeecCChhHHHHHHHhhCCeEEecCC
Q 010746 40 GSEDTVYRYLCPL------RKIGSIIGKGGEIVKQLRSETKSNIRISET 82 (502)
Q Consensus 40 ~~~~~~~~i~vp~------~~~g~iIGk~G~~I~~I~~~tga~I~i~~~ 82 (502)
.+..+.-++.||. .++|+|||+.|.|+|+|+..|+|+|-|-..
T Consensus 144 rpsk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred CcccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 3445667888885 579999999999999999999999999643
No 85
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=95.24 E-value=0.035 Score=42.76 Aligned_cols=34 Identities=38% Similarity=0.561 Sum_probs=30.2
Q ss_pred CCCccEEEEEEeeCCceeeeecCCChHHHHHHhh
Q 010746 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
.....+.++|.+...-+|.||||+|.+|+.|+.-
T Consensus 25 ~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 25 EGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 3467788999999999999999999999999953
No 86
>PRK01064 hypothetical protein; Provisional
Probab=95.21 E-value=0.023 Score=44.23 Aligned_cols=33 Identities=30% Similarity=0.548 Sum_probs=29.9
Q ss_pred CCceEEEEEecCCceeeeecCChhHHHHHHHhh
Q 010746 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (502)
Q Consensus 41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~t 73 (502)
+..+.+++.|..+..|.+|||+|.+|++||.-.
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 566889999999999999999999999998854
No 87
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.09 E-value=0.035 Score=57.03 Aligned_cols=95 Identities=25% Similarity=0.341 Sum_probs=63.0
Q ss_pred CccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEE
Q 010746 271 GNIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITT 349 (502)
Q Consensus 271 ~~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~ 349 (502)
+-+|..||.+|.+|+.|.++. |-+|.+-.-+.+ +..-+..+ +.+.-...+... .......
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~D----------------p~~fI~Na--LsPA~V~~V~i~-~~~~k~a 337 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPD----------------PATYIANA--LSPARVDEVRLV-DPEGRHA 337 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCC----------------HHHHHHHh--cCCceeeEEEEE-cCCCcEE
Confidence 457999999999999999888 667766543311 00111111 111111111000 0112356
Q ss_pred EEEecCCceeeeeCCCchhHHHHHHHhCCeEEEec
Q 010746 350 RILVPSAQIGCLIGRGGAIISEMRSATRASIRILT 384 (502)
Q Consensus 350 ~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 384 (502)
.+.||.++.+..|||+|.+|+--.+.||.+|.|..
T Consensus 338 ~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 338 HVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred EEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 89999999999999999999999999999999954
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.05 E-value=0.044 Score=52.51 Aligned_cols=62 Identities=21% Similarity=0.242 Sum_probs=51.1
Q ss_pred EEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746 143 VRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE 215 (502)
Q Consensus 143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~ 215 (502)
+.+.||.+.++.|||++|.+|+.|.++++++|.+-.. -.|.|.++ .+++.+|+.+|..+-++
T Consensus 147 ~~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~N-----------G~VwI~~~~~~~~~~a~~~I~~~e~~ 209 (235)
T PRK04163 147 TIVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQN-----------GRIWIKGPDEEDEEIAIEAIKKIERE 209 (235)
T ss_pred EEEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcCC-----------cEEEEeeCCHHHHHHHHHHHHHHHhh
Confidence 4578999999999999999999999999999988432 46888886 55788888888765554
No 89
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=94.82 E-value=0.05 Score=57.30 Aligned_cols=94 Identities=22% Similarity=0.321 Sum_probs=63.4
Q ss_pred ccccccccCcccccchhhhc-CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEE
Q 010746 272 NIGGVIGKGGGIIKQIRQES-GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTR 350 (502)
Q Consensus 272 ~~g~IIGk~G~~Ik~i~~~s-ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~ 350 (502)
-+|+.||.+|++|+.|.++. |-+|.+-.-+.+ +..-..-.+.+.-...+..+.. .-...
T Consensus 246 pvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d------------------~~~fi~nal~pa~v~~v~~~~~--~~~~~ 305 (470)
T PRK09202 246 PVGACVGMRGSRIQAISNELGGEKIDIILWSDD------------------PAQFIINALSPAEVSSVVVDED--EHSAD 305 (470)
T ss_pred hhHccCCCCCchHHHHHHHhCCCeEEEEEcCCC------------------HHHHHHHhCCCCEEEEEEEeCC--CCEEE
Confidence 47999999999999999888 667766543211 1111111111111011100111 23678
Q ss_pred EEecCCceeeeeCCCchhHHHHHHHhCCeEEEecC
Q 010746 351 ILVPSAQIGCLIGRGGAIISEMRSATRASIRILTN 385 (502)
Q Consensus 351 i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~ 385 (502)
+.||.++.+..|||+|.+|+-..+.||.+|.|...
T Consensus 306 v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~ 340 (470)
T PRK09202 306 VVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTE 340 (470)
T ss_pred EEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEh
Confidence 99999999999999999999999999999999764
No 90
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=94.80 E-value=0.023 Score=63.06 Aligned_cols=66 Identities=27% Similarity=0.338 Sum_probs=55.4
Q ss_pred ceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 345 PVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 345 ~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
......+.||.+.++.+||.||.+||+|.++||+.|.+. ++-.|.|.+ ..+.+++|+.+|......
T Consensus 552 ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~-----------d~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 552 APRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIE-----------DDGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccC-----------CCceEEEEcccHHHHHHHHHHHHHhccc
Confidence 345677888999999999999999999999999988773 234688888 788999999999887764
No 91
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.78 E-value=0.06 Score=56.12 Aligned_cols=97 Identities=18% Similarity=0.221 Sum_probs=73.0
Q ss_pred cCCCHHHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccC
Q 010746 108 EFVSPAQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCAL 187 (502)
Q Consensus 108 ~~~~~a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~ 187 (502)
+.+.+|.+|-..|++.+...............++...|.|+++....+||.+|...|+|+.+||+.-.+.
T Consensus 564 eal~~a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~vD---------- 633 (760)
T KOG1067|consen 564 EALQKAREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQVD---------- 633 (760)
T ss_pred HHHHhhhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeeec----------
Confidence 4455566777777777665554444445566778889999999999999999999999999999544442
Q ss_pred CCCceEEEec-CHHHHHHHHHHHHHHHhcC
Q 010746 188 SFDELLQVAG-EPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 188 ~~er~v~I~G-~~~~V~~A~~~I~~~l~~~ 216 (502)
+..+.|-- ++.+.++|+..|..++..+
T Consensus 634 --e~t~~i~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 634 --EGTFSIFAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred --CceEEEEecCHHHHHHHHHHHHHHhcCc
Confidence 23466655 5778899999998888764
No 92
>PRK01064 hypothetical protein; Provisional
Probab=94.62 E-value=0.071 Score=41.49 Aligned_cols=34 Identities=35% Similarity=0.477 Sum_probs=29.8
Q ss_pred CCCccEEEEEEeeCCceeeeecCCChHHHHHHhh
Q 010746 136 GELTLITVRMLVPADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 136 ~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
.....+.+++.|...-.|.+|||+|.+|+.|+.-
T Consensus 25 ~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred eCCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 3356688999999999999999999999999864
No 93
>PRK12704 phosphodiesterase; Provisional
Probab=94.50 E-value=0.13 Score=55.06 Aligned_cols=63 Identities=22% Similarity=0.388 Sum_probs=47.4
Q ss_pred EEEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 143 VRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 143 ~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
-.+.+|+ ++.|+|||+.|.+|+.++.-||+.|.|... | ..|.|+| .+-.-+.|...+..++.+
T Consensus 212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iiddt---p-------~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT---P-------EAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcCC---C-------CeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3466776 678999999999999999999999999533 3 4688999 444445666666665554
No 94
>PRK00106 hypothetical protein; Provisional
Probab=94.41 E-value=0.16 Score=54.32 Aligned_cols=64 Identities=22% Similarity=0.423 Sum_probs=50.3
Q ss_pred EEEEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 142 TVRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 142 ~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
.-.+.+|+ ++-|+|||+.|.+|+.++.-|||.+.|... | ..|+|++ +|-.-+-|...+..++.+
T Consensus 226 vs~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt---p-------~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 226 ITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDDT---P-------EVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred eeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcCC---C-------CeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 34467777 678999999999999999999999999533 3 4688999 566666777777776665
No 95
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=94.38 E-value=0.14 Score=54.79 Aligned_cols=64 Identities=22% Similarity=0.391 Sum_probs=49.7
Q ss_pred EEEEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEec-CHHHHHHHHHHHHHHHhc
Q 010746 142 TVRMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAG-EPAVVRKALVQIASRLHE 215 (502)
Q Consensus 142 ~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G-~~~~V~~A~~~I~~~l~~ 215 (502)
.-.+.+|+ ++-|+|||+.|.+|+.++.-|||.|.|... | ..|+|++ +|---+-|...+..++.+
T Consensus 205 ~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iiddt---p-------~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 205 VSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDDT---P-------EAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcCC---C-------CeEEecCCchHHHHHHHHHHHHHHHc
Confidence 34467777 678999999999999999999999999533 3 3688888 566566677777666655
No 96
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=93.45 E-value=0.044 Score=42.19 Aligned_cols=36 Identities=17% Similarity=0.217 Sum_probs=30.7
Q ss_pred CCCceEEEEEecCCceeeeecCChhHHHHHHHhhCC
Q 010746 40 GSEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75 (502)
Q Consensus 40 ~~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga 75 (502)
..+...+.+.|..+..|.||||+|.++++||.-++.
T Consensus 25 ~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 25 EEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp ETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred cCCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 356678888899999999999999999999876543
No 97
>PRK12705 hypothetical protein; Provisional
Probab=92.95 E-value=0.11 Score=55.11 Aligned_cols=64 Identities=25% Similarity=0.266 Sum_probs=45.3
Q ss_pred ceeEEEEEecC-CceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHH
Q 010746 345 PVITTRILVPS-AQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLR 418 (502)
Q Consensus 345 ~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~ 418 (502)
......+.+|. ++-|.||||-|.+|+-+...||+.|.|. +.| +.|+|.+ .|..-+.|...+..+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliid---dtp-------~~V~ls~fdp~rreia~~~l~~L 261 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIID---DTP-------EAVVISSFNPIRREIARLTLEKL 261 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEec---CCc-------cchhhcccCccchHHHHHHHHHH
Confidence 45667788886 5669999999999999999999999994 233 3566666 444444444444333
No 98
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=91.75 E-value=0.37 Score=43.78 Aligned_cols=57 Identities=26% Similarity=0.392 Sum_probs=50.3
Q ss_pred CCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCC
Q 010746 149 ADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENP 217 (502)
Q Consensus 149 ~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~ 217 (502)
+..+|+|+||+|.+--.|++.|.++|.+... .|.|-|..+++.-|...|+.+|.-.+
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad~------------kIHiLG~~~niriAR~avcsLIlGsp 233 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLADS------------KIHILGAFQNIRIARDAVCSLILGSP 233 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecCc------------eEEEeecchhhHHHHHhhHhhhccCC
Confidence 4568999999999999999999999988533 59999999999999999999997643
No 99
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=91.09 E-value=0.77 Score=47.69 Aligned_cols=204 Identities=15% Similarity=0.144 Sum_probs=124.3
Q ss_pred eeecCChhHHHHHHHhhCCeEEec--CCCCCCCccEEEE-EcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCCC
Q 010746 57 SIIGKGGEIVKQLRSETKSNIRIS--ETVPGCDERIVTI-YSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADD 133 (502)
Q Consensus 57 ~iIGk~G~~I~~I~~~tga~I~i~--~~~~~~~ervv~I-~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~ 133 (502)
+|=||+--.+.+|++...|.+.+. +.. | .++.++ .|..- +..+.+..+
T Consensus 393 Fl~gkkngK~TrIm~~v~c~~~~~i~~~~-g--s~~~~~~~g~~~-----------------~F~k~~~~~--------- 443 (657)
T COG5166 393 FLRGKKNGKATRIMKGVSCSELSSIVSST-G--SIVETNGIGEKM-----------------SFSKKLSIP--------- 443 (657)
T ss_pred HhccccCcchhhhhhhcccceeeEEEecC-C--cEEEEeccCcch-----------------hhHHHhcCC---------
Confidence 677777666999999998885543 321 2 243333 22110 111112211
Q ss_pred cCCCCccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746 134 EFGELTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL 213 (502)
Q Consensus 134 ~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l 213 (502)
..+-.-.+.+.||.+.|..|||.||..|++++...++.|++...-++|. + + -
T Consensus 444 --~~EFpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~q---s----------------~-------~ 495 (657)
T COG5166 444 --PTEFPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQ---S----------------Q-------W 495 (657)
T ss_pred --cccCchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcch---h----------------h-------h
Confidence 1122235679999999999999999999999999999998866533332 0 0 1
Q ss_pred hcCCCccccccccCCCCccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhc--
Q 010746 214 HENPSRSQHLLLSSSSNIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQES-- 291 (502)
Q Consensus 214 ~~~~~~~~~~~~~~~~~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~s-- 291 (502)
++ .+-+.+|.+..+.|+|++......+++..
T Consensus 496 ~d-----------------------------------------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f 528 (657)
T COG5166 496 HD-----------------------------------------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRF 528 (657)
T ss_pred hc-----------------------------------------------ceEEECCccCccchhcccccHHHHHhhhccc
Confidence 11 13466888888999998887777776544
Q ss_pred --CCeEEecCCCCCCCCeEEEecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeC---CCc
Q 010746 292 --GASIKVDSSGAEGDDCIIFISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIG---RGG 366 (502)
Q Consensus 292 --ga~I~v~~~~~~~~~~ii~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIG---k~G 366 (502)
...|.|.+. ..+++++-+-. ..++.+.+-- .+ .........+.+|.+.++.-+| -.|
T Consensus 529 ~~Kgdirf~~~----~~sI~~v~~~~------~~I~rv~kne-~v-------~~~~p~~~~~y~~se~h~~g~gena~R~ 590 (657)
T COG5166 529 NLKGDIRFCPQ----STSIFTVDIYS------DEIERVIKNE-TV-------LLEFPAEMHFYVPSEIHKKGIGENAFRG 590 (657)
T ss_pred ccccceEEcCC----ceEEEEEcccc------cHHHHHhhcc-ce-------EEecccccccccchhhhhccCCcccccc
Confidence 234455442 34577766532 2344333311 11 0112355677899999999999 677
Q ss_pred hhHHHHHHHhCCeEEE
Q 010746 367 AIISEMRSATRASIRI 382 (502)
Q Consensus 367 ~~Ik~I~~~tGa~I~i 382 (502)
++|..+.....-.|..
T Consensus 591 ~ni~~~t~~y~~~ie~ 606 (657)
T COG5166 591 ENIQRVTKLYNSYIEF 606 (657)
T ss_pred cchhhhhhhhhcccee
Confidence 7777666655444444
No 100
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.98 E-value=0.083 Score=59.31 Aligned_cols=69 Identities=22% Similarity=0.183 Sum_probs=57.6
Q ss_pred EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (502)
Q Consensus 349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 421 (502)
..+.+|.....+|||++|++|+.++..|||.|.|..- -|. ...+|.+.+.|+++.++.|...|.-.+.+
T Consensus 1342 ~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekm--q~~--Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1342 GKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKM--QPD--NQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccchhhhhhhhccCcchhhhHhhccceEEehhhc--CCc--cchhhhcccCCCChhhhhhhccccceeec
Confidence 4677888889999999999999999999999999651 121 35789999999999999998887766654
No 101
>PRK12705 hypothetical protein; Provisional
Probab=90.84 E-value=0.43 Score=50.71 Aligned_cols=62 Identities=21% Similarity=0.315 Sum_probs=43.2
Q ss_pred EEEeeC-CceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecC-HHHHHHHHHHHHHHHhc
Q 010746 144 RMLVPA-DQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGE-PAVVRKALVQIASRLHE 215 (502)
Q Consensus 144 ~llVp~-~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~-~~~V~~A~~~I~~~l~~ 215 (502)
.+.+|+ ++-|+|||+.|.+|+.++..||+.+.|... | +.|+|++. +..-+.|...+..+|.+
T Consensus 201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliiddt---p-------~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDDT---P-------EAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeecCChHhhccccCccchhHHHHHHhhCCceEecCC---c-------cchhhcccCccchHHHHHHHHHHHhc
Confidence 355665 578999999999999999999999999543 3 24556653 33344555555555544
No 102
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=90.77 E-value=0.36 Score=35.94 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=28.5
Q ss_pred ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeE
Q 010746 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI 77 (502)
Q Consensus 43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I 77 (502)
.....+.+.....|.+|||+|.+|++|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 45566666666789999999999999999997554
No 103
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=90.60 E-value=0.82 Score=50.81 Aligned_cols=21 Identities=14% Similarity=0.366 Sum_probs=12.4
Q ss_pred EEEEEecCCceeeeeCCCchh
Q 010746 348 TTRILVPSAQIGCLIGRGGAI 368 (502)
Q Consensus 348 ~~~i~VP~~~vg~IIGk~G~~ 368 (502)
.+.|.|-.+.+.||+|-.-+.
T Consensus 1085 WIklqIshEaAAcItgLr~Am 1105 (1282)
T KOG0921|consen 1085 WIKLQISHEAAACITGLRPAM 1105 (1282)
T ss_pred eeeEeccHHHHHHHhhhHHHH
Confidence 455666666666666654443
No 104
>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=89.45 E-value=2.2 Score=37.18 Aligned_cols=91 Identities=23% Similarity=0.345 Sum_probs=59.1
Q ss_pred CChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhc-ccCCCcCCCCc
Q 010746 61 KGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAED-SLADDEFGELT 139 (502)
Q Consensus 61 k~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~-~~~~~~~~~~~ 139 (502)
.++..|++|-++..-+|.|-. ++.. +.+-.+|...|.+.+-++. ..+-..+.
T Consensus 23 ~~~dli~~lAk~lrKRIvvR~--------------dps~----------l~~~e~A~~~I~~ivP~ea~i~di~Fd~--- 75 (145)
T cd02410 23 EDGDLVKDLAKDLRKRIVIRP--------------DPSV----------LKPPEEAIKIILEIVPEEAGITDIYFDD--- 75 (145)
T ss_pred cccHHHHHHHHHHhceEEEcC--------------Chhh----------cCCHHHHHHHHHHhCCCccCceeeEecC---
Confidence 467889999988876666632 2211 1123456666665443221 10000011
Q ss_pred cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
.+-++.|-...-|.+||++|.++++|..+||-+-.+.+.
T Consensus 76 -~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 76 -DTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred -CCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 134567778888999999999999999999999999877
No 105
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=88.89 E-value=0.18 Score=38.69 Aligned_cols=33 Identities=18% Similarity=0.300 Sum_probs=27.7
Q ss_pred ccEEEEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (502)
Q Consensus 139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg 171 (502)
....+.+.+..+..|.||||.|.+++.||--.+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHH
Confidence 344777888999999999999999999996544
No 106
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=88.73 E-value=0.21 Score=45.32 Aligned_cols=55 Identities=24% Similarity=0.335 Sum_probs=48.3
Q ss_pred CCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746 355 SAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (502)
Q Consensus 355 ~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 421 (502)
+..+|.|+||+|.+---|.+.|.++|.+.. ..|.|-|..++++.|...|+.+|-.
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIlG 231 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLILG 231 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhcc
Confidence 457899999999998899999999999853 2799999999999999999988733
No 107
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=88.50 E-value=1.1 Score=46.59 Aligned_cols=157 Identities=13% Similarity=0.100 Sum_probs=104.7
Q ss_pred eeeecCCChHHHHHHhhcCceEEEe--ecCCCCcccCCCCce-EEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCC
Q 010746 153 GCVIGKGGQVIQNIRTETRAQIRIL--KDEHLPLCALSFDEL-LQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSS 229 (502)
Q Consensus 153 g~IIGk~G~~Ik~I~~~tga~I~i~--~~~~~p~~~~~~er~-v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~ 229 (502)
-+|-||+--++.+|++...|-+.+. .++ ..++ -.+.|..-+..+++..+.+ +
T Consensus 392 dFl~gkkngK~TrIm~~v~c~~~~~i~~~~--------gs~~~~~~~g~~~~F~k~~~~~~~---E-------------- 446 (657)
T COG5166 392 DFLRGKKNGKATRIMKGVSCSELSSIVSST--------GSIVETNGIGEKMSFSKKLSIPPT---E-------------- 446 (657)
T ss_pred HHhccccCcchhhhhhhcccceeeEEEecC--------CcEEEEeccCcchhhHHHhcCCcc---c--------------
Confidence 3677887777999999988885443 331 1122 2356666666666543321 1
Q ss_pred CccCCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecCCCCCCCCeEE
Q 010746 230 NIYQSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDSSGAEGDDCII 309 (502)
Q Consensus 230 ~~~~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~~~~~~~~~ii 309 (502)
|+ ..+.+.||...|..|||.||..|++...+.++.|.+.....-
T Consensus 447 --Fp----------------------------ae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~------ 490 (657)
T COG5166 447 --FP----------------------------AEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKF------ 490 (657)
T ss_pred --Cc----------------------------hheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhc------
Confidence 11 145678999999999999999999999999998888752210
Q ss_pred EecCCCccCCCchhHHHHHhhCCccccccccCCCCceeEEEEEecCCceeeeeCCCchhHHHHHHHh----CCeEEEecC
Q 010746 310 FISTKEFFEDPSPTITAALRLQPRCSEKTERESGDPVITTRILVPSAQIGCLIGRGGAIISEMRSAT----RASIRILTN 385 (502)
Q Consensus 310 ~i~g~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~t----Ga~I~i~~~ 385 (502)
. +.++ .-..-+..|..-.+.|+|++-.....++++. ...|++.+
T Consensus 491 ----------~----qs~~-----------------~dNV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~- 538 (657)
T COG5166 491 ----------G----QSQW-----------------HDNVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP- 538 (657)
T ss_pred ----------c----hhhh-----------------hcceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC-
Confidence 0 0000 1224577899999999999999988888665 55677732
Q ss_pred CCCCCCCCCCceEEEEEcCHHHHHH
Q 010746 386 ENVPKVAYEDEEMVQITGSLDVASS 410 (502)
Q Consensus 386 ~~~P~~~~~~~r~v~I~G~~~~v~~ 410 (502)
...+.+++-|-.+-+.+
T Consensus 539 --------~~~sI~~v~~~~~~I~r 555 (657)
T COG5166 539 --------QSTSIFTVDIYSDEIER 555 (657)
T ss_pred --------CceEEEEEcccccHHHH
Confidence 23458888876655544
No 108
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=87.86 E-value=0.81 Score=33.94 Aligned_cols=35 Identities=31% Similarity=0.440 Sum_probs=28.3
Q ss_pred cEEEEEEeeCCceeeeecCCChHHHHHHhhcCceE
Q 010746 140 LITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI 174 (502)
Q Consensus 140 ~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I 174 (502)
...+.+.+.....+.+||++|++++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35566677766789999999999999999888544
No 109
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=87.61 E-value=1.2 Score=42.23 Aligned_cols=47 Identities=21% Similarity=0.352 Sum_probs=40.1
Q ss_pred EEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCC
Q 010746 47 RYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEG 99 (502)
Q Consensus 47 ~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~ 99 (502)
-+.||..++-.+|||+|+.++.|.++|+|.|-|... -.|-|.|..+.
T Consensus 149 iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N------G~IWV~~~~~~ 195 (239)
T COG1097 149 IVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN------GRIWVDGENES 195 (239)
T ss_pred EEEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC------CEEEecCCCcc
Confidence 467899999999999999999999999999999654 24788887664
No 110
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.56 E-value=1.7 Score=42.34 Aligned_cols=22 Identities=41% Similarity=0.943 Sum_probs=11.6
Q ss_pred CCCCCCCCC-CCCCCCCCCCCCC
Q 010746 477 YGSYGGSLS-GGGNAYGAYGDHS 498 (502)
Q Consensus 477 yg~yg~~~~-~~~~~yg~~~~~~ 498 (502)
||+||++.+ +-|+||+.+++|+
T Consensus 78 yg~YGgGygg~fGgGyN~~~~~g 100 (362)
T KOG3875|consen 78 YGPYGGGYGGGFGGGYNRFGPYG 100 (362)
T ss_pred CCCcCCCcCcccCcccccccccc
Confidence 345554433 2356666666665
No 111
>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=87.44 E-value=0.53 Score=36.57 Aligned_cols=34 Identities=21% Similarity=0.244 Sum_probs=27.1
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeEE
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIR 78 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~ 78 (502)
.+.+.+..+..|.+|||+|+++.+|+--+..-+.
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 3556666788999999999999999987765444
No 112
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=87.29 E-value=1.1 Score=46.36 Aligned_cols=39 Identities=33% Similarity=0.436 Sum_probs=35.9
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (502)
.+.+.||.+.++.+|||+|.+|++|++..|-+|.|...+
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e 525 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLE 525 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEcc
Confidence 567899999999999999999999999999999998763
No 113
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=87.22 E-value=1 Score=43.85 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCCCC
Q 010746 479 SYGGSLSGGGNAYG 492 (502)
Q Consensus 479 ~yg~~~~~~~~~yg 492 (502)
+||++.+++|+|||
T Consensus 73 ~~G~Gyg~YGgGyg 86 (362)
T KOG3875|consen 73 NYGSGYGPYGGGYG 86 (362)
T ss_pred ccCCCCCCcCCCcC
Confidence 34444333444444
No 114
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=87.06 E-value=1.1 Score=42.95 Aligned_cols=51 Identities=12% Similarity=0.193 Sum_probs=45.9
Q ss_pred eeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhc
Q 010746 153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHE 215 (502)
Q Consensus 153 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~ 215 (502)
-+|||.+|.+++.|+--|.|-|-|... .|.+.|....+..+...|.+.+.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence 569999999999999999999998544 699999999999999999988876
No 115
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=87.01 E-value=2.4 Score=44.36 Aligned_cols=95 Identities=24% Similarity=0.393 Sum_probs=65.2
Q ss_pred eecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCCCcCCC
Q 010746 58 IIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGE 137 (502)
Q Consensus 58 iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~ 137 (502)
++=+.|..|++|-++..-+|.|-.+ +.. +++..+|...|++.+-++.--.+- .
T Consensus 43 ~~~~~~dlik~lAk~lrKRI~iR~d--------------Psv----------l~~~e~A~~~I~eivP~ea~i~~i---~ 95 (637)
T COG1782 43 LFAKDGDLIKDLAKDLRKRIIIRPD--------------PSV----------LKPPEEARKIILEIVPEEAGITDI---Y 95 (637)
T ss_pred HhccchhHHHHHHHHHhhceEeccC--------------chh----------cCCHHHHHHHHHHhCccccCceeE---E
Confidence 4557889999999998777776433 111 223567777777655332211110 0
Q ss_pred CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
-...+-+++|-.+.-|.+|||+|++.++|..+||-.-+|.+.
T Consensus 96 Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~ 137 (637)
T COG1782 96 FDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRT 137 (637)
T ss_pred ecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeec
Confidence 011245678888999999999999999999999998888876
No 116
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=86.76 E-value=0.28 Score=55.35 Aligned_cols=60 Identities=20% Similarity=0.155 Sum_probs=51.5
Q ss_pred CCceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC-CCCCCCccEEEEEcCCCCc
Q 010746 41 SEDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE-TVPGCDERIVTIYSSSEGT 100 (502)
Q Consensus 41 ~~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~-~~~~~~ervv~I~G~~e~~ 100 (502)
.+....++-+|......|||++|.+|+.++.-|||.|.|.. ...+..||.+++.|.++.+
T Consensus 1337 ~~~~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~ 1397 (2131)
T KOG4369|consen 1337 VPANQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQ 1397 (2131)
T ss_pred CcccccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhh
Confidence 34555778889999999999999999999999999999986 4445789999999998764
No 117
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=86.56 E-value=0.75 Score=35.74 Aligned_cols=33 Identities=27% Similarity=0.509 Sum_probs=26.7
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceE
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI 174 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I 174 (502)
.+.+.+..+..|.||||.|+++..||--.+.-+
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~ 57 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVL 57 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHH
Confidence 456777888999999999999999996655433
No 118
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=86.52 E-value=0.95 Score=47.61 Aligned_cols=68 Identities=18% Similarity=0.237 Sum_probs=57.4
Q ss_pred CCceeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEc-CHHHHHHHHHHHHHHHHh
Q 010746 343 GDPVITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITG-SLDVASSALSQVTLRLRA 421 (502)
Q Consensus 343 ~~~~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G-~~~~v~~A~~~I~~~l~~ 421 (502)
....+...+.|+.+....+||.+|-..|.|..+||+.-.+ ++..|+|.- ++.+.+.|+.+|...+..
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 4567888999999999999999999999999999965555 234788877 788999999999988877
Q ss_pred c
Q 010746 422 N 422 (502)
Q Consensus 422 ~ 422 (502)
.
T Consensus 661 ~ 661 (760)
T KOG1067|consen 661 D 661 (760)
T ss_pred c
Confidence 3
No 119
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.98 E-value=0.52 Score=35.82 Aligned_cols=37 Identities=27% Similarity=0.491 Sum_probs=29.7
Q ss_pred EEEEeeCCc-----eeeeecCCChHHHHHHhhc-CceEEEeec
Q 010746 143 VRMLVPADQ-----IGCVIGKGGQVIQNIRTET-RAQIRILKD 179 (502)
Q Consensus 143 ~~llVp~~~-----vg~IIGk~G~~Ik~I~~~t-ga~I~i~~~ 179 (502)
+.+.|-+.. +|..||++|..|+.|+++. |-+|.|...
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 456666766 8999999999999999999 999999765
No 120
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=85.90 E-value=0.61 Score=35.42 Aligned_cols=36 Identities=25% Similarity=0.488 Sum_probs=27.8
Q ss_pred EEEEecCCc-----eeeeeCCCchhHHHHHHHh-CCeEEEec
Q 010746 349 TRILVPSAQ-----IGCLIGRGGAIISEMRSAT-RASIRILT 384 (502)
Q Consensus 349 ~~i~VP~~~-----vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~ 384 (502)
..+.|-... +|..||++|++|+.|.++. |-+|+|-.
T Consensus 5 ~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 5 TKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 345555555 8999999999999999999 88898854
No 121
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=84.19 E-value=2.1 Score=41.06 Aligned_cols=51 Identities=20% Similarity=0.221 Sum_probs=43.6
Q ss_pred eeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHHh
Q 010746 359 GCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLRA 421 (502)
Q Consensus 359 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~~ 421 (502)
-++||.+|++++.|+-.|.|.|-|+.. +|.+.|....++.+...+.+.+..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~------------TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN------------TVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc------------EEEeecCcchHHHHHHHHHHHHhc
Confidence 367999999999999999999999643 799999999888887777776654
No 122
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=83.64 E-value=3.2 Score=39.30 Aligned_cols=47 Identities=17% Similarity=0.403 Sum_probs=39.6
Q ss_pred EEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHH
Q 010746 349 TRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLD 406 (502)
Q Consensus 349 ~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~ 406 (502)
.-+.||+..|-.+||++|+.++-|.+.|+|+|-|-.+ -.|-|.+..+
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 5688999999999999999999999999999998543 2566777655
No 123
>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=83.24 E-value=0.55 Score=36.48 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=29.4
Q ss_pred eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEE
Q 010746 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIR 78 (502)
Q Consensus 44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~ 78 (502)
....+.+.....+.|||++|++|++|.++..-.+.
T Consensus 25 ~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 25 DQIIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp SEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred CeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 45678888999999999999999999887765553
No 124
>PRK13764 ATPase; Provisional
Probab=83.17 E-value=1.3 Score=48.21 Aligned_cols=43 Identities=23% Similarity=0.405 Sum_probs=38.7
Q ss_pred eEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCC
Q 010746 347 ITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVP 389 (502)
Q Consensus 347 ~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P 389 (502)
....+.||.+.++.+|||+|.+|++|.+..|.+|.|...++.|
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 4677899999999999999999999999999999998776654
No 125
>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=82.58 E-value=0.76 Score=36.14 Aligned_cols=37 Identities=14% Similarity=0.292 Sum_probs=31.3
Q ss_pred eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEec
Q 010746 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRIS 80 (502)
Q Consensus 44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~ 80 (502)
..+++.|-...-|.|||++|+.|++|+++..-...+.
T Consensus 30 ~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 30 TRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred CeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 3478888889999999999999999999887666654
No 126
>PRK13764 ATPase; Provisional
Probab=82.54 E-value=3.1 Score=45.42 Aligned_cols=43 Identities=30% Similarity=0.440 Sum_probs=38.2
Q ss_pred EEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCC
Q 010746 141 ITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLP 183 (502)
Q Consensus 141 ~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p 183 (502)
-.+.+.||.+.++.+|||+|.+|++|.++.|..|.|...+..|
T Consensus 481 ~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 481 NKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred CeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 3677899999999999999999999999999999998775443
No 127
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=82.34 E-value=0.83 Score=47.17 Aligned_cols=38 Identities=24% Similarity=0.368 Sum_probs=34.4
Q ss_pred eEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC
Q 010746 44 TVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE 81 (502)
Q Consensus 44 ~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~ 81 (502)
-...+.||.+.++.+|||+|.+|++|++..|-+|.|-.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~ 523 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKP 523 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEE
Confidence 34668899999999999999999999999999999964
No 128
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=81.20 E-value=1.9 Score=38.68 Aligned_cols=36 Identities=31% Similarity=0.422 Sum_probs=30.0
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecC
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISE 81 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~ 81 (502)
.+-++|-... |.-|||+|++|++|++..|-+|.+-+
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE 97 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVE 97 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEE
Confidence 3456666666 99999999999999999998888743
No 129
>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=80.89 E-value=0.73 Score=35.78 Aligned_cols=33 Identities=39% Similarity=0.634 Sum_probs=28.4
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceE
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQI 174 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I 174 (502)
.+.+.+...+.+.|||++|++|++|++...-.+
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 567889999999999999999999997766554
No 130
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=77.39 E-value=3.1 Score=37.43 Aligned_cols=37 Identities=24% Similarity=0.504 Sum_probs=32.4
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeec
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKD 179 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~ 179 (502)
.+-++|.... |..|||+|.+|+++++..|-+|.+...
T Consensus 62 rvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 62 LVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred EEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 4557777777 999999999999999999999999765
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=77.28 E-value=3.3 Score=36.15 Aligned_cols=38 Identities=26% Similarity=0.401 Sum_probs=32.0
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET 82 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~ 82 (502)
+=++.|-.++-|.+|||+|.+++.|..+||-+-.|-..
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 34567778899999999999999999999987777544
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=75.43 E-value=10 Score=41.81 Aligned_cols=96 Identities=23% Similarity=0.432 Sum_probs=61.5
Q ss_pred eecCChhHHHHHHHhhCCeEEecCCCCCCCccEEEEEcCCCCcccccCCccCCCHHHHHHHHHHHHHhhhcccCCCcCCC
Q 010746 58 IIGKGGEIVKQLRSETKSNIRISETVPGCDERIVTIYSSSEGTNLFEDSGEFVSPAQDALFRVHDRIVAEDSLADDEFGE 137 (502)
Q Consensus 58 iIGk~G~~I~~I~~~tga~I~i~~~~~~~~ervv~I~G~~e~~~~~~~~~~~~~~a~~al~~i~~~i~~~~~~~~~~~~~ 137 (502)
.+=.++..|++|-++..-+|.|-.+ +.. +.+-.+|...|.+.+-++.--.+ - .
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~--------------~~~----------~~~~~~~~~~i~~~~~~~~~~~~-~--~ 89 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPD--------------PSV----------LLPPEEAIEKIKEIVPEEAGITD-I--Y 89 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecC--------------hhh----------cCCHHHHHHHHHHhCCCcCCcee-E--E
Confidence 3446778899998888766665322 211 11234566666554432210000 0 0
Q ss_pred CccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecC
Q 010746 138 LTLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDE 180 (502)
Q Consensus 138 ~~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~ 180 (502)
=...+-+++|-.+.-|.+|||+|.++++|..+||-+-+|.+..
T Consensus 90 f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 90 FDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred ecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 0112456778888899999999999999999999999998873
No 133
>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=75.03 E-value=3.6 Score=32.30 Aligned_cols=35 Identities=14% Similarity=0.380 Sum_probs=29.3
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEE
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 176 (502)
.+++.|....-|.|||++|+.|++|++...-...+
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 47788888889999999999999999886655544
No 134
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.64 E-value=2.8 Score=34.94 Aligned_cols=32 Identities=28% Similarity=0.314 Sum_probs=26.7
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCe
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSN 76 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~ 76 (502)
.+++.|-...-|.|||++|++|++|++.....
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 36777888889999999999999998876443
No 135
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=70.85 E-value=11 Score=39.58 Aligned_cols=96 Identities=24% Similarity=0.317 Sum_probs=66.9
Q ss_pred eeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcCCCccccccccCCCCcc
Q 010746 153 GCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHENPSRSQHLLLSSSSNIY 232 (502)
Q Consensus 153 g~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~~~~~~~~~~~~~~~~~ 232 (502)
..++-+.|..|++|-++..-+|.|-++ |..- ..-+.|.+.|.+++-++..-.. +
T Consensus 41 P~~~~~~~dlik~lAk~lrKRI~iR~d---Psvl-------------~~~e~A~~~I~eivP~ea~i~~-i--------- 94 (637)
T COG1782 41 PELFAKDGDLIKDLAKDLRKRIIIRPD---PSVL-------------KPPEEARKIILEIVPEEAGITD-I--------- 94 (637)
T ss_pred HHHhccchhHHHHHHHHHhhceEeccC---chhc-------------CCHHHHHHHHHHhCccccCcee-E---------
Confidence 456778999999999999999999776 3210 1235688888887755421100 0
Q ss_pred CCCCccccCCCcCCCCCCCcccCccccccceEEEeccCCccccccccCcccccchhhhcCCeEEecC
Q 010746 233 QSSGVYLSAPLVGSYGNYSARRDEASAREFSLRLVCPAGNIGGVIGKGGGIIKQIRQESGASIKVDS 299 (502)
Q Consensus 233 ~~gg~~~~~p~~~~~~~~~~~~~~~~~~~~~~~i~vp~~~~g~IIGk~G~~Ik~i~~~sga~I~v~~ 299 (502)
.-+..+-++.|-.+.-|.+|||+|++.++|..++|-.-++-.
T Consensus 95 -------------------------~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR 136 (637)
T COG1782 95 -------------------------YFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVR 136 (637)
T ss_pred -------------------------EecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeee
Confidence 011123356777788899999999999999999996655544
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=68.20 E-value=5 Score=31.78 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=23.3
Q ss_pred EEEEecCCceeeeecCChhHHHHHHHhh
Q 010746 46 YRYLCPLRKIGSIIGKGGEIVKQLRSET 73 (502)
Q Consensus 46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~t 73 (502)
+++.|....-|.+||++|++|++|++..
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 5555556888999999999999998875
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=65.32 E-value=5 Score=37.91 Aligned_cols=32 Identities=28% Similarity=0.366 Sum_probs=27.3
Q ss_pred ceEEEEEecCCceeeeecCChhHHHHHHHhhC
Q 010746 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETK 74 (502)
Q Consensus 43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tg 74 (502)
....++.|....-|.||||+|+.|++|+++..
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~ 81 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKELE 81 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHHHH
Confidence 44577888899999999999999999987654
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=64.18 E-value=6.2 Score=32.88 Aligned_cols=30 Identities=30% Similarity=0.528 Sum_probs=24.8
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg 171 (502)
.+++.|....-|.|||++|+.|++|++...
T Consensus 62 ~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~ 91 (109)
T cd02412 62 RVEVTIHTARPGIIIGKKGAGIEKLRKELQ 91 (109)
T ss_pred CEEEEEEeCCCCcccCCchHHHHHHHHHHH
Confidence 366777788889999999999999987644
No 139
>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=61.37 E-value=9.1 Score=30.26 Aligned_cols=28 Identities=29% Similarity=0.554 Sum_probs=22.8
Q ss_pred EEEEeeCCceeeeecCCChHHHHHHhhc
Q 010746 143 VRMLVPADQIGCVIGKGGQVIQNIRTET 170 (502)
Q Consensus 143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~t 170 (502)
+++.|....-|.+||++|+.|++|++..
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 5566666888999999999999988653
No 140
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=57.41 E-value=9 Score=36.21 Aligned_cols=30 Identities=30% Similarity=0.505 Sum_probs=25.0
Q ss_pred eeEEEEEecCCceeeeeCCCchhHHHHHHH
Q 010746 346 VITTRILVPSAQIGCLIGRGGAIISEMRSA 375 (502)
Q Consensus 346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~ 375 (502)
...+.|.|....-|.|||++|+.|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 345778888889999999999999987654
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=52.73 E-value=17 Score=35.48 Aligned_cols=30 Identities=30% Similarity=0.390 Sum_probs=23.8
Q ss_pred cEEEEEEee-CCceeeeecCCChHHHHHHhh
Q 010746 140 LITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 140 ~~~~~llVp-~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
.+.+.++|. .++.+.||||+|++||+|..+
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ 250 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIA 250 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHH
Confidence 356677777 557899999999999988654
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=51.96 E-value=19 Score=35.17 Aligned_cols=32 Identities=28% Similarity=0.377 Sum_probs=25.3
Q ss_pred ceeEEEEEec-CCceeeeeCCCchhHHHHHHHh
Q 010746 345 PVITTRILVP-SAQIGCLIGRGGAIISEMRSAT 376 (502)
Q Consensus 345 ~~~~~~i~VP-~~~vg~IIGk~G~~Ik~I~~~t 376 (502)
..+...+.|. .++-+-|||++|++||+|...+
T Consensus 219 ~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 219 LKIHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 3477888888 4566999999999999876554
No 143
>PF09869 DUF2096: Uncharacterized protein conserved in archaea (DUF2096); InterPro: IPR017098 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=51.26 E-value=44 Score=29.84 Aligned_cols=57 Identities=18% Similarity=0.256 Sum_probs=43.5
Q ss_pred ccEEEEEEeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHH
Q 010746 139 TLITVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRL 213 (502)
Q Consensus 139 ~~~~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l 213 (502)
..-++|+-+|...+- +.+++|.+-+|+-+.+ .+ +..|.|.|..+.|.+|++.++.+.
T Consensus 111 ~~~~iRv~l~~~i~~-------erl~ei~E~~gvI~Ef-ee----------~~~V~I~Gdke~Ik~aLKe~s~~w 167 (169)
T PF09869_consen 111 GFETIRVKLKKPIQE-------ERLQEISEWHGVIFEF-EE----------DDKVVIEGDKERIKKALKEFSSFW 167 (169)
T ss_pred CceeEEEecCccchH-------HHHHHHHHHhceeEEe-cC----------CcEEEEeccHHHHHHHHHHHHHHh
Confidence 344666666665542 5678999999998888 22 346999999999999999987654
No 144
>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=50.98 E-value=3.7e+02 Score=29.41 Aligned_cols=63 Identities=21% Similarity=0.348 Sum_probs=37.6
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHH------hhcCceEEEeecCC--CCc---ccCCCCceEEEecCHHHHHHHHHHHH
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIR------TETRAQIRILKDEH--LPL---CALSFDELLQVAGEPAVVRKALVQIA 210 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~------~~tga~I~i~~~~~--~p~---~~~~~er~v~I~G~~~~V~~A~~~I~ 210 (502)
..++++|+ ..++|| +++++. +++|+.|.-..... ++. .....-..+.+.|++++++++.+.+-
T Consensus 304 ~e~VV~~~---S~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~lG 377 (562)
T TIGR03802 304 TKDVVLTN---KEYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQLG 377 (562)
T ss_pred EEEEEECC---cccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHHcC
Confidence 33344444 455654 788886 36787776654422 221 11122346899999999999876644
No 145
>COG1159 Era GTPase [General function prediction only]
Probab=48.41 E-value=21 Score=35.11 Aligned_cols=31 Identities=35% Similarity=0.531 Sum_probs=23.6
Q ss_pred ccEEEEEEee-CCceeeeecCCChHHHHHHhh
Q 010746 139 TLITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 139 ~~~~~~llVp-~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
..+...++|+ .++-+-||||+|++||+|-..
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~ 258 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTA 258 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHH
Confidence 3455667777 457899999999999877543
No 146
>cd07055 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view.
Probab=48.22 E-value=42 Score=24.71 Aligned_cols=40 Identities=13% Similarity=0.112 Sum_probs=27.3
Q ss_pred HHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHH
Q 010746 373 RSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTL 417 (502)
Q Consensus 373 ~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~ 417 (502)
.+.+++.| +.....+|. ..-.+.|.|...+|+.|+..+.+
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 444445553 34467799999999999888765
No 147
>PRK15494 era GTPase Era; Provisional
Probab=47.18 E-value=23 Score=35.95 Aligned_cols=29 Identities=24% Similarity=0.415 Sum_probs=22.9
Q ss_pred EEEEEEee-CCceeeeecCCChHHHHHHhh
Q 010746 141 ITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 141 ~~~~llVp-~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
+.+.|+|. .++-+.||||+|++||+|..+
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ 302 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAK 302 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHH
Confidence 55677777 457899999999999887643
No 148
>PRK15494 era GTPase Era; Provisional
Probab=44.90 E-value=29 Score=35.23 Aligned_cols=37 Identities=19% Similarity=0.339 Sum_probs=27.9
Q ss_pred eeEEEEEecC-CceeeeeCCCchhHHHHHHH--------hCCeEEE
Q 010746 346 VITTRILVPS-AQIGCLIGRGGAIISEMRSA--------TRASIRI 382 (502)
Q Consensus 346 ~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~--------tGa~I~i 382 (502)
.+...|.|.. ++-+-|||++|++||+|... .+++|.+
T Consensus 272 ~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l 317 (339)
T PRK15494 272 KINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHL 317 (339)
T ss_pred EEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 4678888984 56699999999999977544 4665554
No 149
>PRK00089 era GTPase Era; Reviewed
Probab=44.85 E-value=26 Score=34.46 Aligned_cols=29 Identities=41% Similarity=0.704 Sum_probs=22.5
Q ss_pred EEEEEEee-CCceeeeecCCChHHHHHHhh
Q 010746 141 ITVRMLVP-ADQIGCVIGKGGQVIQNIRTE 169 (502)
Q Consensus 141 ~~~~llVp-~~~vg~IIGk~G~~Ik~I~~~ 169 (502)
+.+.|.|. .++.+.||||+|++||+|..+
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 55666676 557899999999999887644
No 150
>PRK03818 putative transporter; Validated
Probab=44.85 E-value=2.9e+02 Score=30.11 Aligned_cols=135 Identities=16% Similarity=0.174 Sum_probs=71.1
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCC------------CCCCCccEEEEEcCCCCcccccCCccCCCH
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISET------------VPGCDERIVTIYSSSEGTNLFEDSGEFVSP 112 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~------------~~~~~ervv~I~G~~e~~~~~~~~~~~~~~ 112 (502)
..++.|+++. ++ |++++++.......+.|..- ..=....++.|.|..++
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~------------- 266 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPED------------- 266 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHH-------------
Confidence 3666677443 34 67899999888766665311 11122466788886443
Q ss_pred HHHHHHHHHHHHhhhcccCCCcCCCCccEEEEEEeeCCceeeeecCCChHHHHH--HhhcCceEEEeecC--CCCc---c
Q 010746 113 AQDALFRVHDRIVAEDSLADDEFGELTLITVRMLVPADQIGCVIGKGGQVIQNI--RTETRAQIRILKDE--HLPL---C 185 (502)
Q Consensus 113 a~~al~~i~~~i~~~~~~~~~~~~~~~~~~~~llVp~~~vg~IIGk~G~~Ik~I--~~~tga~I~i~~~~--~~p~---~ 185 (502)
+.++.+..-.+. ..+.+.........++++|+ ..++|| +++++ ++++|+.|.=.... .++. .
T Consensus 267 ----l~~l~~~~Gl~~-~~~~~~~~~~~~~E~Vvv~~---S~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~l~~~~d~ 335 (552)
T PRK03818 267 ----LHKAQLVIGEEV-DTSLSTRGTDLRSERVVVTN---EKVLGK---KLRDLHLKNKYGVVISRLNRAGVELVASPDL 335 (552)
T ss_pred ----HHHHHHhcCCcc-CccccccCcceEEEEEEEcC---hhccCC---cHHHhcccccCCeEEEEEeECCeecCCCCCC
Confidence 333333222111 00001111223334444454 366665 77777 47778766554432 1211 0
Q ss_pred cCCCCceEEEecCHHHHHHHHHHH
Q 010746 186 ALSFDELLQVAGEPAVVRKALVQI 209 (502)
Q Consensus 186 ~~~~er~v~I~G~~~~V~~A~~~I 209 (502)
....-..+.+.|+++++++..+.+
T Consensus 336 ~Lq~GD~LlVvG~~~~i~~l~~~L 359 (552)
T PRK03818 336 SLQFGDILNLVGRPEAIDAVANVL 359 (552)
T ss_pred EEecCCEEEEEECHHHHHHHHHHh
Confidence 111224589999999999977643
No 151
>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=44.73 E-value=22 Score=39.26 Aligned_cols=42 Identities=29% Similarity=0.463 Sum_probs=34.9
Q ss_pred ceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEecCCCC
Q 010746 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRISETVP 84 (502)
Q Consensus 43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i~~~~~ 84 (502)
..+=+++|-.++-|.||||+|+++++|.++||-+-.|-...|
T Consensus 92 ~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~ 133 (630)
T TIGR03675 92 DVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPP 133 (630)
T ss_pred CCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCC
Confidence 344567888899999999999999999999998888765543
No 152
>COG1159 Era GTPase [General function prediction only]
Probab=44.57 E-value=29 Score=34.17 Aligned_cols=34 Identities=35% Similarity=0.549 Sum_probs=25.9
Q ss_pred CCceeEEEEEecC-CceeeeeCCCchhHHHHHHHh
Q 010746 343 GDPVITTRILVPS-AQIGCLIGRGGAIISEMRSAT 376 (502)
Q Consensus 343 ~~~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~t 376 (502)
....+...+.|+. ++-+-||||+|++||+|-..+
T Consensus 225 ~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 225 GLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred CeEEEEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 3455677888984 566999999999999775444
No 153
>PRK00089 era GTPase Era; Reviewed
Probab=44.30 E-value=28 Score=34.26 Aligned_cols=38 Identities=26% Similarity=0.496 Sum_probs=28.3
Q ss_pred ceeEEEEEec-CCceeeeeCCCchhHHHHHHH--------hCCeEEE
Q 010746 345 PVITTRILVP-SAQIGCLIGRGGAIISEMRSA--------TRASIRI 382 (502)
Q Consensus 345 ~~~~~~i~VP-~~~vg~IIGk~G~~Ik~I~~~--------tGa~I~i 382 (502)
..+...|.|. .++-+-|||++|++|++|... .+++|.+
T Consensus 224 ~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l 270 (292)
T PRK00089 224 VRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFL 270 (292)
T ss_pred EEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEE
Confidence 3467788887 456699999999999977554 4666555
No 154
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=43.25 E-value=16 Score=33.94 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=30.3
Q ss_pred CceEEEEEecCCceeeeecCChhHHHHHHHhhCCeEEe
Q 010746 42 EDTVYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNIRI 79 (502)
Q Consensus 42 ~~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I~i 79 (502)
..-.+.+.+-.+..+.|||+.|+++..||--+.+-+.-
T Consensus 89 ~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 89 EGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred cCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 44456667777779999999999999999988765554
No 155
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=40.20 E-value=29 Score=34.46 Aligned_cols=34 Identities=35% Similarity=0.586 Sum_probs=27.5
Q ss_pred CccEEEEEEeeC-CceeeeecCCChHHHHHHhhcC
Q 010746 138 LTLITVRMLVPA-DQIGCVIGKGGQVIQNIRTETR 171 (502)
Q Consensus 138 ~~~~~~~llVp~-~~vg~IIGk~G~~Ik~I~~~tg 171 (502)
...+..++++|. ++...||||+|..|++|-.+-+
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 456778899995 5678899999999999877654
No 156
>CHL00048 rps3 ribosomal protein S3
Probab=39.45 E-value=28 Score=32.85 Aligned_cols=32 Identities=9% Similarity=0.063 Sum_probs=26.6
Q ss_pred ceEEEEEecCCceeeeecCChhHHHHHHHhhC
Q 010746 43 DTVYRYLCPLRKIGSIIGKGGEIVKQLRSETK 74 (502)
Q Consensus 43 ~~~~~i~vp~~~~g~iIGk~G~~I~~I~~~tg 74 (502)
...+++.|-...-|.|||++|++|++|++...
T Consensus 65 ~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 65 IDLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CCeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 34467777788889999999999999998764
No 157
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=39.21 E-value=27 Score=32.68 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=25.0
Q ss_pred EEEEecCCceeeeecCChhHHHHHHHhhCCe
Q 010746 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETKSN 76 (502)
Q Consensus 46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~ 76 (502)
.++.|-...-|.+||++|++|++|++...-.
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 5555555889999999999999998887543
No 158
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=39.14 E-value=38 Score=31.50 Aligned_cols=35 Identities=17% Similarity=0.338 Sum_probs=28.2
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcCceEEE
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETRAQIRI 176 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i 176 (502)
.+.+-+..+..+.|||+.|.++..||--+++-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 45667777789999999999999999777665443
No 159
>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=38.65 E-value=29 Score=32.13 Aligned_cols=31 Identities=19% Similarity=0.417 Sum_probs=26.4
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCC
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKS 75 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga 75 (502)
..++.|....-|.|||++|+.|++|+++..-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k 69 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKLQK 69 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHHHH
Confidence 4778888888999999999999999887643
No 160
>COG4010 Uncharacterized protein conserved in archaea [Function unknown]
Probab=38.09 E-value=1e+02 Score=26.84 Aligned_cols=43 Identities=26% Similarity=0.344 Sum_probs=35.2
Q ss_pred hHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHh
Q 010746 161 QVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLH 214 (502)
Q Consensus 161 ~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~ 214 (502)
+.++.|-+..|+-|.+... ..|.|.|..+.|.+|++.|...-.
T Consensus 126 eRlqDi~E~hgvIiE~~E~-----------D~V~i~Gd~drVk~aLke~~~~wk 168 (170)
T COG4010 126 ERLQDIAETHGVIIEFEEY-----------DLVAIYGDSDRVKKALKEIGSFWK 168 (170)
T ss_pred HHHHHHHHhhheeEEeeec-----------cEEEEeccHHHHHHHHHHHHHHHh
Confidence 4567788889998888633 379999999999999999987643
No 161
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=36.93 E-value=35 Score=33.89 Aligned_cols=34 Identities=29% Similarity=0.493 Sum_probs=26.8
Q ss_pred CceeEEEEEecC-CceeeeeCCCchhHHHHHHHhC
Q 010746 344 DPVITTRILVPS-AQIGCLIGRGGAIISEMRSATR 377 (502)
Q Consensus 344 ~~~~~~~i~VP~-~~vg~IIGk~G~~Ik~I~~~tG 377 (502)
...+..++.+|. ++.-.|||++|..|++|-++-+
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 456778888995 5667899999999999866543
No 162
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.46 E-value=33 Score=32.40 Aligned_cols=33 Identities=12% Similarity=0.257 Sum_probs=27.0
Q ss_pred EEEEEecCCceeeeecCChhHHHHHHHhhCCeE
Q 010746 45 VYRYLCPLRKIGSIIGKGGEIVKQLRSETKSNI 77 (502)
Q Consensus 45 ~~~i~vp~~~~g~iIGk~G~~I~~I~~~tga~I 77 (502)
.+++.|-...-|.|||++|..|++|+++..-.+
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~ 77 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQKRF 77 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHHHHh
Confidence 367777778889999999999999988875443
No 163
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=33.87 E-value=97 Score=31.31 Aligned_cols=51 Identities=22% Similarity=0.197 Sum_probs=42.1
Q ss_pred cCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010746 354 PSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT 416 (502)
Q Consensus 354 P~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 416 (502)
+.+..-.+.|..+.+++.|.+..|+.|.... +.++|+|+...|..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVARG------------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeCC------------ceEEEEechHHHHHHHHHHh
Confidence 3566678999999999999999999887632 37999999878888877666
No 164
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=32.04 E-value=1e+02 Score=30.93 Aligned_cols=19 Identities=26% Similarity=0.485 Sum_probs=7.5
Q ss_pred CCCCCCCCCCCCCCCCCCC
Q 010746 452 YGNRDNQSRGRGNSYATGN 470 (502)
Q Consensus 452 ~~~~~~~~~g~g~~~~~g~ 470 (502)
|+++++.+.|+|...++||
T Consensus 366 ~gGrGgGRGggG~GGGggy 384 (465)
T KOG3973|consen 366 WGGRGGGRGGGGRGGGGGY 384 (465)
T ss_pred CCCCCCCCCCCCCCCCCCC
Confidence 3444333333333344555
No 165
>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=31.04 E-value=51 Score=30.55 Aligned_cols=29 Identities=28% Similarity=0.605 Sum_probs=24.1
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhc
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTET 170 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~t 170 (502)
.+++.|....-+.|||++|..|++|++.-
T Consensus 39 ~~~I~I~~~rPg~vIG~~g~~i~~l~~~l 67 (195)
T TIGR01008 39 GTKVIIFAERPGLVIGRGGRRIRELTEKL 67 (195)
T ss_pred cEEEEEEECCCceEECCCchHHHHHHHHH
Confidence 46777888888999999999999888653
No 166
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=29.95 E-value=1.4e+02 Score=24.69 Aligned_cols=40 Identities=25% Similarity=0.278 Sum_probs=31.5
Q ss_pred hhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHHHHHhcC
Q 010746 168 TETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 168 ~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~~~l~~~ 216 (502)
+..++.|-|... + .-.+.|+|+..+|+.|+..|.+.+++.
T Consensus 61 Kaa~V~igF~DR--F-------sGslvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 61 KAADVHIGFLDR--F-------SGALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred hccCcEEeeeec--c-------ceeEEEEccHHHHHHHHHHHHHHHHhh
Confidence 345677777655 2 235999999999999999999999873
No 167
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=29.51 E-value=1.7e+02 Score=29.44 Aligned_cols=10 Identities=30% Similarity=0.105 Sum_probs=4.3
Q ss_pred HHHHHHHHHH
Q 010746 204 KALVQIASRL 213 (502)
Q Consensus 204 ~A~~~I~~~l 213 (502)
.|+.++...|
T Consensus 103 ~a~~lLlsyL 112 (465)
T KOG3973|consen 103 SAKKLLLSYL 112 (465)
T ss_pred HHHHHHHHHH
Confidence 3444444444
No 168
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=29.17 E-value=55 Score=30.64 Aligned_cols=29 Identities=31% Similarity=0.576 Sum_probs=23.2
Q ss_pred EEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746 143 VRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (502)
Q Consensus 143 ~~llVp~~~vg~IIGk~G~~Ik~I~~~tg 171 (502)
+++.|....-|.+||++|++|++|++...
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 55566668889999999999999886643
No 169
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=29.14 E-value=53 Score=31.03 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=24.1
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhcC
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTETR 171 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~tg 171 (502)
.+++.|....-|.|||++|..|++|++...
T Consensus 45 ~i~V~I~tarPg~vIG~~G~~i~~l~~~L~ 74 (220)
T PTZ00084 45 RTEIIIRATRTREVLGDKGRRIRELTSLLQ 74 (220)
T ss_pred cEEEEEEECCCccEEcCCchHHHHHHHHHH
Confidence 366777777789999999999998886543
No 170
>CHL00048 rps3 ribosomal protein S3
Probab=28.88 E-value=57 Score=30.74 Aligned_cols=29 Identities=10% Similarity=0.253 Sum_probs=24.1
Q ss_pred EEEEEeeCCceeeeecCCChHHHHHHhhc
Q 010746 142 TVRMLVPADQIGCVIGKGGQVIQNIRTET 170 (502)
Q Consensus 142 ~~~llVp~~~vg~IIGk~G~~Ik~I~~~t 170 (502)
.+++.|-...-+.|||++|+.|++|++..
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L 95 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINL 95 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHH
Confidence 46677777788999999999999988764
No 171
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=26.42 E-value=1.3e+02 Score=30.35 Aligned_cols=53 Identities=13% Similarity=0.168 Sum_probs=43.4
Q ss_pred EeeCCceeeeecCCChHHHHHHhhcCceEEEeecCCCCcccCCCCceEEEecCHHHHHHHHHHHH
Q 010746 146 LVPADQIGCVIGKGGQVIQNIRTETRAQIRILKDEHLPLCALSFDELLQVAGEPAVVRKALVQIA 210 (502)
Q Consensus 146 lVp~~~vg~IIGk~G~~Ik~I~~~tga~I~i~~~~~~p~~~~~~er~v~I~G~~~~V~~A~~~I~ 210 (502)
+-+....-.|.|..+..++.|.+.+|+.|.... +.++|+|+...|..|...+.
T Consensus 20 ~~~~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG------------~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 20 LSDDNELVALFGPTDTNLSLLEIALGVSIVARG------------EAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred cCCchhhhhhcCCCCccHHHHHHHhCcEEEeCC------------ceEEEEechHHHHHHHHHHh
Confidence 344667888999999999999999998887632 35999999878888877776
No 172
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.65 E-value=68 Score=30.14 Aligned_cols=29 Identities=28% Similarity=0.459 Sum_probs=24.7
Q ss_pred EEEEecCCceeeeecCChhHHHHHHHhhC
Q 010746 46 YRYLCPLRKIGSIIGKGGEIVKQLRSETK 74 (502)
Q Consensus 46 ~~i~vp~~~~g~iIGk~G~~I~~I~~~tg 74 (502)
+++.|-...-+.|||++|..|++|++...
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 66777777889999999999999987653
No 173
>PF02080 TrkA_C: TrkA-C domain; InterPro: IPR006037 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the C-terminal subdomain of RCK.; GO: 0008324 cation transmembrane transporter activity, 0006813 potassium ion transport; PDB: 2BKP_A 1VCT_A 2BKO_A 2BKN_A 3L4B_C 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A ....
Probab=23.35 E-value=1.2e+02 Score=22.23 Aligned_cols=49 Identities=18% Similarity=0.343 Sum_probs=32.5
Q ss_pred ChHHHH--HHhhcCceEEEeecCC---CC--cccCCCCceEEEecCHHHHHHHHHH
Q 010746 160 GQVIQN--IRTETRAQIRILKDEH---LP--LCALSFDELLQVAGEPAVVRKALVQ 208 (502)
Q Consensus 160 G~~Ik~--I~~~tga~I~i~~~~~---~p--~~~~~~er~v~I~G~~~~V~~A~~~ 208 (502)
|.+|++ +++.+++.|.-...+. .| .........|.|.|..+.+.++...
T Consensus 14 gk~l~el~l~~~~~~~i~~i~R~~~~~~p~~~~~l~~gD~l~v~g~~~~i~~~~~~ 69 (71)
T PF02080_consen 14 GKTLKELDLPERYGVRIVAIKRGGEIIIPDGDTVLQAGDILIVVGDPEDIERFREL 69 (71)
T ss_dssp TEBHHHCTHHCHHTEEEEEEEETEEEES--TT-BE-TTEEEEEEEEHHHHHHHHHH
T ss_pred CCCHHHCCCCccCCEEEEEEEECCEEECCCCCCEECCCCEEEEEECHHHHHHHHHh
Confidence 577888 7788888877665431 12 1222334579999999999988754
No 174
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=21.89 E-value=2.4e+02 Score=31.79 Aligned_cols=7 Identities=14% Similarity=0.610 Sum_probs=3.5
Q ss_pred eEEEEEc
Q 010746 397 EMVQITG 403 (502)
Q Consensus 397 r~v~I~G 403 (502)
+.+.+.|
T Consensus 755 ~a~~l~G 761 (931)
T KOG2044|consen 755 PAIRLDG 761 (931)
T ss_pred hhhhcCC
Confidence 3455555
No 175
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=20.94 E-value=2.9e+02 Score=22.79 Aligned_cols=50 Identities=16% Similarity=0.109 Sum_probs=32.9
Q ss_pred HhhcCceEEEeecCC-CCcccC---CCCceEEEec-CHHHHHHHHHHHHHHHhcC
Q 010746 167 RTETRAQIRILKDEH-LPLCAL---SFDELLQVAG-EPAVVRKALVQIASRLHEN 216 (502)
Q Consensus 167 ~~~tga~I~i~~~~~-~p~~~~---~~er~v~I~G-~~~~V~~A~~~I~~~l~~~ 216 (502)
.+.+++.|-+.++-- -..+.. +.+-++.|.| ++..|+.|++.+.+.|++.
T Consensus 46 tKaa~vev~~~~~f~gGa~h~~~~~sG~vi~ii~G~dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 46 TKAAEVEVVYARSFYAGAAHASTPLAGEVIGILAGPSPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred hhhcCeEEEEEeecccccccCccCCCccEEEEEeCCCHHHHHHHHHHHHHHHhcc
Confidence 356777777665510 011111 3444566999 9999999999999988763
No 176
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=20.53 E-value=2.7e+02 Score=21.22 Aligned_cols=42 Identities=17% Similarity=0.253 Sum_probs=29.0
Q ss_pred chhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHH
Q 010746 366 GAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVT 416 (502)
Q Consensus 366 G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~ 416 (502)
-..|.+|-+.++|+|.=.. .+.-+|+++|+++.+...+.++.
T Consensus 16 r~ei~~l~~~f~a~ivd~~---------~~~~iie~tG~~~kid~fi~~l~ 57 (75)
T PF10369_consen 16 RSEILQLAEIFRARIVDVS---------PDSIIIELTGTPEKIDAFIKLLK 57 (75)
T ss_dssp HHHHHHHHHHTT-EEEEEE---------TTEEEEEEEE-HHHHHHHHHHST
T ss_pred HHHHHHHHHHhCCEEEEEC---------CCEEEEEEcCCHHHHHHHHHHhh
Confidence 3457888899999864433 24468999999999998766543
No 177
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=20.45 E-value=2.3e+02 Score=21.35 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=33.9
Q ss_pred ChHHHHHHhhcCceEEEeecCC--CCcccCCCCceEEEecCHHHHHHHHHHHHH
Q 010746 160 GQVIQNIRTETRAQIRILKDEH--LPLCALSFDELLQVAGEPAVVRKALVQIAS 211 (502)
Q Consensus 160 G~~Ik~I~~~tga~I~i~~~~~--~p~~~~~~er~v~I~G~~~~V~~A~~~I~~ 211 (502)
...|.+|..+++..+.|....- +-.. .-..-++.+.|+.+.+++|+..+.+
T Consensus 16 ~piis~l~~~~~v~~nIl~g~i~~i~~~-~~G~l~l~l~g~~~~~~~a~~~L~~ 68 (76)
T PF09383_consen 16 EPIISQLIREFGVDVNILHGNIEEIQGT-PFGILILELPGDDEEIEKAIAYLRE 68 (76)
T ss_dssp SCHHHHHHHHHT-EEEEEEEEEEEETTE-EEEEEEEEEES-HHHHHHHHHHHHH
T ss_pred chHHHHHHHHhCCCEEEEEEEeEEcCCe-eEEEEEEEEECCHHHHHHHHHHHHH
Confidence 4678999999999999976511 0000 0112368899999999999987765
No 178
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=20.10 E-value=1.6e+02 Score=24.40 Aligned_cols=25 Identities=32% Similarity=0.276 Sum_probs=23.0
Q ss_pred EEEEEcCHHHHHHHHHHHHHHHHhc
Q 010746 398 MVQITGSLDVASSALSQVTLRLRAN 422 (502)
Q Consensus 398 ~v~I~G~~~~v~~A~~~I~~~l~~~ 422 (502)
.+.|+|...+|+.|+..+.+.+++.
T Consensus 76 slvitGdvs~Ve~Al~~V~~~l~~~ 100 (111)
T PRK15468 76 ALVIYGSVGAVEEALSQTVSGLGRL 100 (111)
T ss_pred eEEEEccHHHHHHHHHHHHHHHHhh
Confidence 6889999999999999999999874
No 179
>COG0490 Putative regulatory, ligand-binding protein related to C-terminal domains of K+ channels [Inorganic ion transport and metabolism]
Probab=20.08 E-value=2.1e+02 Score=25.67 Aligned_cols=59 Identities=24% Similarity=0.209 Sum_probs=36.0
Q ss_pred ecCCceeeeeCCCchhHHHHHHHhCCeE-EEecCCCCCCCCC-----CCceEEEEEcCHHHHHHHHHHHH
Q 010746 353 VPSAQIGCLIGRGGAIISEMRSATRASI-RILTNENVPKVAY-----EDEEMVQITGSLDVASSALSQVT 416 (502)
Q Consensus 353 VP~~~vg~IIGk~G~~Ik~I~~~tGa~I-~i~~~~~~P~~~~-----~~~r~v~I~G~~~~v~~A~~~I~ 416 (502)
.-+..+|.=||- -.|+++|||.| -|.++.++=..++ ....++.+.|+...+..++.+..
T Consensus 94 ~~s~~~GksiGd-----l~irq~TGaTIIAI~r~~e~I~SPgPy~vle~gDtlvviG~~~~~~r~~~f~~ 158 (162)
T COG0490 94 AGSPFIGKTIGD-----LNIRQNTGATVIAIVRNEEKILSPGPYTVLEAGDTLVVIGEETGLKRAKRFLL 158 (162)
T ss_pred cCCcccCcchhh-----cccccccCcEEEEEEecCcEecCCCchhhhcCCCEEEEEecchHhHHHHHHhh
Confidence 334455555553 56899999884 4544433211111 22347889999999998876543
No 180
>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=20.02 E-value=2.7e+02 Score=21.84 Aligned_cols=69 Identities=16% Similarity=0.125 Sum_probs=46.1
Q ss_pred eeEEEEEecCCceeeeeCCCchhHHHHHHHhCCeEEEecCCCCCCCCCCCceEEEEEcCHHHHHHHHHHHHHHHH
Q 010746 346 VITTRILVPSAQIGCLIGRGGAIISEMRSATRASIRILTNENVPKVAYEDEEMVQITGSLDVASSALSQVTLRLR 420 (502)
Q Consensus 346 ~~~~~i~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~P~~~~~~~r~v~I~G~~~~v~~A~~~I~~~l~ 420 (502)
..+..+..-.+ |-+- |=..+.+|-+..+++++..-+|...- ...+.+++|.|+..++..|-+.++..|.
T Consensus 17 ~~~a~i~are~--gV~a--G~~~~~~i~~~l~~~v~~~~~dG~~v--~~g~~i~~i~G~a~~ll~~ER~~LN~l~ 85 (88)
T PF02749_consen 17 TGTATIIARED--GVLA--GLEEAEEIFEKLGLEVEWLVKDGDRV--EPGDVILEIEGPARALLTAERTALNFLQ 85 (88)
T ss_dssp EEEEEEEESSS--EEE---SHHHHHHHHHHCTEEEEESS-TT-EE--ETTCEEEEEEEEHHHHHHHHHHHHHHHH
T ss_pred EEEEEEEeCCC--EEEE--CHHHHHHHHhhccEEEEEEeCCCCCc--cCCcEEEEEEeCHHHHHHHHHHHHHHHH
Confidence 34444444444 3332 55777888888899988765543221 2456899999999999999888877764
Done!