Query 007603
Match_columns 596
No_of_seqs 250 out of 1960
Neff 7.2
Searched_HMMs 46136
Date Thu Mar 28 12:51:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007603hhsearch_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 2.8E-43 6E-48 381.1 32.9 370 19-446 37-415 (485)
2 KOG2193 IGF-II mRNA-binding pr 100.0 4E-42 8.8E-47 349.5 21.8 368 18-442 192-566 (584)
3 KOG1676 K-homology type RNA bi 100.0 2.1E-40 4.5E-45 353.0 29.8 338 23-443 52-392 (600)
4 KOG2192 PolyC-binding hnRNP-K 100.0 5.9E-32 1.3E-36 261.6 23.4 333 20-440 43-384 (390)
5 KOG2193 IGF-II mRNA-binding pr 100.0 8.5E-29 1.8E-33 252.6 12.5 260 128-461 198-505 (584)
6 KOG1676 K-homology type RNA bi 100.0 4E-28 8.7E-33 259.3 17.8 245 127-441 52-301 (600)
7 KOG2191 RNA-binding protein NO 99.9 3.1E-26 6.8E-31 228.1 20.5 239 19-311 33-281 (402)
8 KOG2191 RNA-binding protein NO 99.9 5.7E-23 1.2E-27 205.0 17.9 250 128-439 38-314 (402)
9 KOG2190 PolyC-binding proteins 99.8 6.5E-20 1.4E-24 199.4 22.6 165 273-442 42-210 (485)
10 KOG2192 PolyC-binding hnRNP-K 99.6 2.2E-15 4.8E-20 146.8 10.1 147 128-350 47-194 (390)
11 TIGR03665 arCOG04150 arCOG0415 99.5 2.3E-13 5E-18 130.2 9.6 138 29-201 2-152 (172)
12 TIGR03665 arCOG04150 arCOG0415 99.4 5.9E-13 1.3E-17 127.4 11.0 141 278-440 2-151 (172)
13 PRK13763 putative RNA-processi 99.4 8E-13 1.7E-17 127.4 11.5 142 25-201 3-158 (180)
14 PRK13763 putative RNA-processi 99.4 3.3E-12 7.3E-17 123.1 12.2 147 274-441 3-158 (180)
15 cd02396 PCBP_like_KH K homolog 99.3 4.3E-12 9.4E-17 101.8 6.8 65 367-435 1-65 (65)
16 cd02396 PCBP_like_KH K homolog 99.3 3.4E-12 7.5E-17 102.4 6.2 65 130-195 1-65 (65)
17 KOG2279 Kinase anchor protein 99.3 3.8E-11 8.2E-16 128.2 12.5 269 16-326 59-351 (608)
18 KOG2279 Kinase anchor protein 99.2 5.3E-11 1.2E-15 127.1 10.7 231 126-437 65-365 (608)
19 cd02394 vigilin_like_KH K homo 99.2 4.7E-11 1E-15 94.7 6.4 60 368-434 2-61 (62)
20 PF00013 KH_1: KH domain syndr 99.1 4.2E-11 9E-16 94.4 4.3 60 367-434 1-60 (60)
21 cd02393 PNPase_KH Polynucleoti 99.1 1.8E-10 3.9E-15 91.1 7.1 58 366-434 2-60 (61)
22 cd00105 KH-I K homology RNA-bi 99.1 4.7E-10 1E-14 89.1 7.3 62 368-434 2-63 (64)
23 KOG2208 Vigilin [Lipid transpo 99.0 1.8E-09 3.8E-14 124.5 13.7 320 24-440 200-562 (753)
24 cd02394 vigilin_like_KH K homo 99.0 3.7E-10 8E-15 89.6 4.9 60 131-194 2-61 (62)
25 PF00013 KH_1: KH domain syndr 99.0 1.6E-10 3.5E-15 91.0 2.7 60 130-194 1-60 (60)
26 cd00105 KH-I K homology RNA-bi 98.9 1.8E-09 3.8E-14 85.8 6.5 62 131-194 2-63 (64)
27 cd02393 PNPase_KH Polynucleoti 98.9 2.2E-09 4.8E-14 84.9 6.6 58 129-194 2-60 (61)
28 KOG2208 Vigilin [Lipid transpo 98.8 5.6E-09 1.2E-13 120.5 8.2 286 25-439 347-634 (753)
29 PF13014 KH_3: KH domain 98.8 8.8E-09 1.9E-13 75.5 5.4 42 35-76 1-43 (43)
30 smart00322 KH K homology RNA-b 98.8 3.6E-08 7.8E-13 78.4 8.7 66 366-438 3-68 (69)
31 PF13014 KH_3: KH domain 98.8 9.9E-09 2.2E-13 75.3 4.8 43 376-422 1-43 (43)
32 smart00322 KH K homology RNA-b 98.6 1.2E-07 2.5E-12 75.4 7.8 67 128-198 2-68 (69)
33 COG1094 Predicted RNA-binding 98.5 1.8E-07 3.8E-12 89.5 6.9 141 23-201 6-165 (194)
34 COG1094 Predicted RNA-binding 98.5 8.4E-07 1.8E-11 84.9 9.9 143 274-440 8-164 (194)
35 cd02395 SF1_like-KH Splicing f 98.1 7E-06 1.5E-10 73.9 6.9 67 375-441 15-96 (120)
36 cd02395 SF1_like-KH Splicing f 98.0 1.3E-05 2.9E-10 72.0 6.7 64 138-201 15-96 (120)
37 PRK08406 transcription elongat 97.8 4E-05 8.7E-10 70.9 6.3 103 26-165 33-135 (140)
38 TIGR02696 pppGpp_PNP guanosine 97.7 0.00016 3.5E-09 82.5 9.9 93 334-440 549-642 (719)
39 KOG2113 Predicted RNA binding 97.6 6.8E-05 1.5E-09 75.8 4.8 148 272-436 24-179 (394)
40 KOG2113 Predicted RNA binding 97.6 0.00014 3E-09 73.7 6.5 155 23-198 24-181 (394)
41 PRK08406 transcription elongat 97.5 0.00026 5.6E-09 65.5 7.5 102 274-402 32-135 (140)
42 TIGR02696 pppGpp_PNP guanosine 97.5 0.0003 6.4E-09 80.4 9.2 94 98-200 548-642 (719)
43 TIGR01952 nusA_arch NusA famil 97.3 0.00042 9.1E-09 64.1 6.0 102 26-165 34-136 (141)
44 TIGR03591 polynuc_phos polyrib 97.1 0.0011 2.5E-08 76.6 8.4 91 336-439 523-614 (684)
45 TIGR03591 polynuc_phos polyrib 97.1 0.0011 2.4E-08 76.7 7.4 94 99-200 521-615 (684)
46 TIGR01952 nusA_arch NusA famil 97.0 0.0026 5.6E-08 58.9 7.9 101 275-402 34-136 (141)
47 KOG0119 Splicing factor 1/bran 96.9 0.0029 6.2E-08 68.1 8.5 73 128-200 137-230 (554)
48 COG0195 NusA Transcription elo 96.7 0.0038 8.3E-08 60.6 6.5 101 28-166 79-179 (190)
49 PLN00207 polyribonucleotide nu 96.5 0.0033 7E-08 73.7 5.8 95 98-200 654-750 (891)
50 COG1185 Pnp Polyribonucleotide 96.5 0.005 1.1E-07 69.3 6.9 99 334-445 522-621 (692)
51 PLN00207 polyribonucleotide nu 96.5 0.0049 1.1E-07 72.3 7.1 92 336-440 657-750 (891)
52 KOG1588 RNA-binding protein Sa 96.5 0.0028 6.1E-08 63.5 4.3 40 22-61 89-134 (259)
53 COG1185 Pnp Polyribonucleotide 96.5 0.0091 2E-07 67.3 8.6 95 98-200 521-616 (692)
54 KOG0119 Splicing factor 1/bran 96.4 0.0077 1.7E-07 65.0 7.1 78 365-442 137-232 (554)
55 KOG0336 ATP-dependent RNA heli 96.4 0.003 6.5E-08 66.8 4.0 65 366-438 47-111 (629)
56 KOG2814 Transcription coactiva 96.4 0.0031 6.8E-08 65.0 4.0 70 128-201 56-126 (345)
57 cd02134 NusA_KH NusA_K homolog 96.4 0.0053 1.2E-07 48.5 4.4 37 24-60 24-60 (61)
58 KOG1588 RNA-binding protein Sa 96.3 0.021 4.5E-07 57.4 9.4 82 363-444 89-191 (259)
59 KOG0336 ATP-dependent RNA heli 96.3 0.0048 1E-07 65.3 4.7 72 123-199 41-112 (629)
60 COG0195 NusA Transcription elo 96.1 0.0037 8E-08 60.7 2.9 102 275-404 77-180 (190)
61 TIGR01953 NusA transcription t 96.1 0.011 2.4E-07 62.7 6.5 95 34-166 243-338 (341)
62 PRK12327 nusA transcription el 96.0 0.014 3.1E-07 62.3 6.7 96 34-167 245-341 (362)
63 PRK12329 nusA transcription el 95.9 0.011 2.4E-07 63.9 5.7 95 34-166 277-372 (449)
64 PRK12328 nusA transcription el 95.9 0.014 2.9E-07 62.2 5.9 95 34-167 251-346 (374)
65 KOG2814 Transcription coactiva 95.8 0.012 2.6E-07 60.7 5.2 71 365-441 56-126 (345)
66 cd02134 NusA_KH NusA_K homolog 95.8 0.013 2.8E-07 46.2 4.1 36 366-401 25-60 (61)
67 PRK11824 polynucleotide phosph 95.5 0.022 4.7E-07 66.3 6.2 93 335-440 525-618 (693)
68 PRK04163 exosome complex RNA-b 95.4 0.027 5.8E-07 56.9 6.0 64 367-441 146-210 (235)
69 PRK11824 polynucleotide phosph 95.4 0.015 3.3E-07 67.5 4.6 94 99-200 524-618 (693)
70 PRK00468 hypothetical protein; 95.3 0.021 4.4E-07 47.1 3.7 35 21-55 26-60 (75)
71 TIGR01953 NusA transcription t 95.2 0.015 3.2E-07 61.7 3.5 97 282-404 242-339 (341)
72 PRK09202 nusA transcription el 95.0 0.035 7.7E-07 61.4 5.8 94 34-166 245-339 (470)
73 PRK02821 hypothetical protein; 94.7 0.033 7.2E-07 46.1 3.5 36 21-56 27-62 (77)
74 PRK12328 nusA transcription el 94.7 0.021 4.6E-07 60.8 2.8 98 283-407 251-349 (374)
75 PRK12327 nusA transcription el 94.4 0.023 5E-07 60.8 2.3 98 282-405 244-342 (362)
76 COG5176 MSL5 Splicing factor ( 94.3 0.14 3.1E-06 49.5 7.1 41 23-63 146-192 (269)
77 PRK12704 phosphodiesterase; Pr 94.2 0.12 2.7E-06 58.1 7.6 68 364-441 208-277 (520)
78 COG1837 Predicted RNA-binding 94.1 0.057 1.2E-06 44.4 3.5 54 104-157 4-58 (76)
79 PRK12329 nusA transcription el 94.1 0.13 2.9E-06 55.8 7.2 94 282-403 276-372 (449)
80 PF14611 SLS: Mitochondrial in 94.0 1.4 2.9E-05 43.6 14.0 86 104-200 5-90 (210)
81 PRK01064 hypothetical protein; 94.0 0.068 1.5E-06 44.3 3.8 34 22-55 27-60 (78)
82 PRK00468 hypothetical protein; 93.9 0.063 1.4E-06 44.2 3.5 34 363-396 27-60 (75)
83 COG1837 Predicted RNA-binding 93.9 0.067 1.5E-06 44.0 3.6 33 22-54 27-59 (76)
84 TIGR03319 YmdA_YtgF conserved 93.8 0.17 3.7E-06 56.9 7.7 65 364-438 202-268 (514)
85 PRK02821 hypothetical protein; 93.7 0.087 1.9E-06 43.6 4.0 32 126-157 28-59 (77)
86 PRK09202 nusA transcription el 93.5 0.042 9.2E-07 60.8 2.3 96 283-405 245-341 (470)
87 PRK00106 hypothetical protein; 93.4 0.21 4.6E-06 56.0 7.6 65 364-438 223-289 (535)
88 PRK01064 hypothetical protein; 93.3 0.095 2.1E-06 43.5 3.6 33 125-157 26-58 (78)
89 COG5176 MSL5 Splicing factor ( 93.2 0.32 6.9E-06 47.2 7.4 42 363-404 145-192 (269)
90 TIGR03319 YmdA_YtgF conserved 93.2 0.27 5.8E-06 55.3 8.1 65 129-200 204-270 (514)
91 PRK04163 exosome complex RNA-b 93.2 0.14 3.1E-06 51.6 5.4 62 132-201 148-210 (235)
92 PRK00106 hypothetical protein; 93.1 0.32 6.9E-06 54.7 8.4 66 128-200 224-291 (535)
93 PRK12704 phosphodiesterase; Pr 92.9 0.3 6.5E-06 55.0 7.9 63 131-200 212-276 (520)
94 KOG1067 Predicted RNA-binding 92.7 0.48 1E-05 52.4 8.8 92 101-201 569-661 (760)
95 PF14611 SLS: Mitochondrial in 92.7 1.3 2.8E-05 43.7 11.4 127 277-439 29-164 (210)
96 PF13083 KH_4: KH domain; PDB: 90.2 0.15 3.3E-06 41.6 1.5 35 22-56 26-60 (73)
97 KOG4369 RTK signaling protein 90.1 0.2 4.2E-06 59.2 2.7 71 366-440 1340-1410(2131)
98 cd02409 KH-II KH-II (K homolo 89.5 0.59 1.3E-05 36.6 4.4 35 24-58 24-58 (68)
99 KOG4369 RTK signaling protein 89.3 0.23 4.9E-06 58.7 2.4 63 25-87 1340-1403(2131)
100 KOG1067 Predicted RNA-binding 88.4 1.1 2.4E-05 49.6 6.8 91 336-440 569-660 (760)
101 KOG3273 Predicted RNA-binding 86.9 0.36 7.9E-06 46.5 1.8 54 374-439 177-230 (252)
102 PF13184 KH_5: NusA-like KH do 86.8 0.69 1.5E-05 37.5 3.1 39 367-405 4-48 (69)
103 PF13184 KH_5: NusA-like KH do 86.5 0.55 1.2E-05 38.0 2.4 35 28-62 6-46 (69)
104 cd02409 KH-II KH-II (K homolo 85.9 1.2 2.6E-05 34.8 4.1 35 365-399 24-58 (68)
105 KOG3273 Predicted RNA-binding 85.9 0.69 1.5E-05 44.7 3.1 57 136-201 176-232 (252)
106 PRK12705 hypothetical protein; 84.5 1.3 2.9E-05 49.5 5.1 62 132-200 201-264 (508)
107 PF13083 KH_4: KH domain; PDB: 84.4 0.48 1E-05 38.5 1.2 36 364-399 27-62 (73)
108 PF07650 KH_2: KH domain syndr 82.0 0.82 1.8E-05 37.6 1.7 33 27-59 27-59 (78)
109 PRK13764 ATPase; Provisional 80.6 1.8 3.9E-05 49.5 4.3 45 364-408 479-523 (602)
110 cd02413 40S_S3_KH K homology R 80.5 1.1 2.4E-05 37.5 2.0 35 27-61 32-66 (81)
111 KOG2874 rRNA processing protei 80.2 1.9 4.2E-05 43.8 3.8 51 141-200 161-211 (356)
112 cd02414 jag_KH jag_K homology 80.2 1.8 3.9E-05 35.6 3.1 34 27-60 26-59 (77)
113 PRK06418 transcription elongat 79.5 2 4.2E-05 41.0 3.5 32 29-61 65-96 (166)
114 COG1855 ATPase (PilT family) [ 78.6 1.7 3.6E-05 47.5 3.0 41 366-406 486-526 (604)
115 cd02414 jag_KH jag_K homology 78.0 2.1 4.6E-05 35.2 2.9 35 367-401 25-59 (77)
116 PRK12705 hypothetical protein; 77.0 3.7 8E-05 46.0 5.3 40 364-403 196-236 (508)
117 COG1855 ATPase (PilT family) [ 75.8 1.8 4E-05 47.2 2.4 38 26-63 487-524 (604)
118 KOG2874 rRNA processing protei 74.9 5.5 0.00012 40.6 5.3 51 378-440 161-211 (356)
119 COG1097 RRP4 RNA-binding prote 74.6 6.3 0.00014 39.6 5.6 48 367-425 147-194 (239)
120 COG1097 RRP4 RNA-binding prote 74.6 5.5 0.00012 40.0 5.2 57 133-197 150-207 (239)
121 cd02410 archeal_CPSF_KH The ar 74.3 4.3 9.3E-05 37.7 4.1 38 130-167 77-114 (145)
122 PF07650 KH_2: KH domain syndr 74.2 1.5 3.2E-05 36.1 1.0 35 366-400 25-59 (78)
123 COG5166 Uncharacterized conser 73.4 13 0.00028 41.2 8.0 103 275-430 450-556 (657)
124 cd02412 30S_S3_KH K homology R 72.0 3.6 7.8E-05 36.4 3.0 31 27-57 63-93 (109)
125 PRK13764 ATPase; Provisional 71.4 3.4 7.3E-05 47.4 3.3 37 26-62 482-518 (602)
126 cd02411 archeal_30S_S3_KH K ho 69.4 5.1 0.00011 33.7 3.2 29 27-55 40-68 (85)
127 COG1782 Predicted metal-depend 67.8 11 0.00025 41.7 6.1 97 38-168 42-138 (637)
128 COG0092 RpsC Ribosomal protein 66.2 5.1 0.00011 40.1 3.0 31 26-56 52-82 (233)
129 PRK06418 transcription elongat 63.1 9.6 0.00021 36.3 4.1 38 366-404 61-98 (166)
130 COG1782 Predicted metal-depend 62.8 11 0.00024 41.7 5.0 98 287-406 42-139 (637)
131 cd02413 40S_S3_KH K homology R 60.9 6.1 0.00013 33.0 2.1 35 130-164 31-65 (81)
132 cd02410 archeal_CPSF_KH The ar 59.9 10 0.00022 35.2 3.5 96 289-407 21-117 (145)
133 COG5166 Uncharacterized conser 53.2 12 0.00026 41.5 3.1 131 283-439 389-523 (657)
134 TIGR03675 arCOG00543 arCOG0054 50.0 17 0.00036 42.2 4.0 39 130-168 94-132 (630)
135 cd02411 archeal_30S_S3_KH K ho 48.1 12 0.00026 31.4 1.8 27 131-157 40-66 (85)
136 TIGR03675 arCOG00543 arCOG0054 48.0 31 0.00068 40.0 5.8 97 288-407 37-134 (630)
137 COG0092 RpsC Ribosomal protein 46.8 12 0.00025 37.6 1.8 30 128-157 50-79 (233)
138 cd02412 30S_S3_KH K homology R 46.4 17 0.00037 32.0 2.7 30 367-396 62-91 (109)
139 PF00936 BMC: BMC domain; Int 41.3 29 0.00062 28.4 3.0 36 414-449 38-73 (75)
140 cd07053 BMC_PduT_repeat1 1,2-p 39.4 38 0.00082 28.0 3.5 37 414-450 37-73 (76)
141 TIGR00436 era GTP-binding prot 38.8 35 0.00075 34.9 3.9 30 25-54 221-251 (270)
142 TIGR01008 rpsC_E_A ribosomal p 38.5 31 0.00068 33.8 3.3 31 27-57 40-70 (195)
143 PRK04191 rps3p 30S ribosomal p 38.0 31 0.00068 34.1 3.3 32 27-58 42-73 (207)
144 TIGR00436 era GTP-binding prot 38.0 31 0.00067 35.3 3.4 32 365-396 220-252 (270)
145 CHL00048 rps3 ribosomal protei 37.1 33 0.00072 34.2 3.3 32 26-57 67-98 (214)
146 PTZ00084 40S ribosomal protein 35.9 35 0.00075 34.2 3.2 33 27-59 46-78 (220)
147 COG1159 Era GTPase [General fu 34.6 21 0.00046 37.1 1.5 33 364-396 227-260 (298)
148 PRK03818 putative transporter; 33.9 2.3E+02 0.0051 32.4 9.9 131 26-193 206-358 (552)
149 PRK15494 era GTPase Era; Provi 33.4 39 0.00085 35.9 3.4 30 366-395 273-303 (339)
150 PRK00089 era GTPase Era; Revie 32.7 40 0.00088 34.7 3.3 30 366-395 226-256 (292)
151 PRK15494 era GTPase Era; Provi 31.5 51 0.0011 35.1 3.9 30 25-54 273-303 (339)
152 PRK00089 era GTPase Era; Revie 29.1 60 0.0013 33.4 3.9 30 25-54 226-256 (292)
153 TIGR03802 Asp_Ala_antiprt aspa 28.9 3.3E+02 0.0072 31.2 10.1 58 130-193 304-375 (562)
154 KOG1423 Ras-like GTPase ERA [C 28.6 49 0.0011 34.8 3.0 34 363-396 325-359 (379)
155 cd07045 BMC_CcmK_like Carbon d 27.4 79 0.0017 26.6 3.5 36 415-450 38-75 (84)
156 COG1159 Era GTPase [General fu 26.7 74 0.0016 33.2 3.9 30 25-54 229-259 (298)
157 cd07056 BMC_PduK 1,2-propanedi 26.2 80 0.0017 26.1 3.3 36 414-449 38-75 (77)
158 COG1847 Jag Predicted RNA-bind 25.9 55 0.0012 32.3 2.6 70 365-441 90-159 (208)
159 KOG1423 Ras-like GTPase ERA [C 25.8 63 0.0014 34.1 3.1 40 17-56 317-360 (379)
160 COG1702 PhoH Phosphate starvat 25.3 1.4E+02 0.0031 31.8 5.8 51 373-435 22-72 (348)
161 cd07054 BMC_PduT_repeat2 1,2-p 24.1 92 0.002 25.8 3.3 35 415-449 40-76 (78)
162 TIGR01009 rpsC_bact ribosomal 23.9 73 0.0016 31.7 3.1 30 27-56 64-93 (211)
163 COG1847 Jag Predicted RNA-bind 23.9 58 0.0013 32.2 2.4 35 26-60 92-126 (208)
164 PRK15468 carboxysome structura 21.9 1.8E+02 0.004 25.7 4.7 41 393-442 61-101 (111)
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=2.8e-43 Score=381.14 Aligned_cols=370 Identities=28% Similarity=0.447 Sum_probs=294.4
Q ss_pred CCCCCcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCc
Q 007603 19 NLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEV 98 (596)
Q Consensus 19 ~~~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~ 98 (596)
..++...+|||||+.+.+|.||||+|.+|++||++|.++|+|.+..+++.|||++|+|...+ ...
T Consensus 37 ~~p~~t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~---------------~~~ 101 (485)
T KOG2190|consen 37 TGPDETLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVE---------------LNL 101 (485)
T ss_pred CCCCCcceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEeccccc---------------ccC
Confidence 34444556999999999999999999999999999999999999999999999999997322 257
Q ss_pred cHHHHHHHHHHHHHHhhhhccC-----CC-CCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCC
Q 007603 99 SSTQEAVIRVFERMWEVEAEVE-----GD-GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAA 172 (596)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~-----~~-~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~ 172 (596)
+++++|++++++.+.....+++ .. ......+++|||||..++|+||||+|+.||+|+++|||+|+|.++ ..|.
T Consensus 102 ~~~~~al~ka~~~iv~~~~~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~ 180 (485)
T KOG2190|consen 102 SPATDALFKAFDMIVFKLEEDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN 180 (485)
T ss_pred CchHHHHHHHHHHHhhcccccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc
Confidence 8899999999999887533221 11 112226899999999999999999999999999999999999996 7788
Q ss_pred CCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCC---CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCC
Q 007603 173 IDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK---SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNAS 249 (596)
Q Consensus 173 ~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~---~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~ 249 (596)
+++|.|+|.|.+++|.+|+..|..+|++++.+.- ....+|+|... .+...+|.......+++
T Consensus 181 ster~V~IsG~~~av~~al~~Is~~L~~~~~~~~~~~~st~~y~P~~~--------------~~~~~~~s~~~~~~~~~- 245 (485)
T KOG2190|consen 181 STERAVTISGEPDAVKKALVQISSRLLENPPRSPPPLVSTIPYRPSAS--------------QGGPVLPSTAQTSPDAH- 245 (485)
T ss_pred ccceeEEEcCchHHHHHHHHHHHHHHHhcCCcCCCCCCCcccCCCccc--------------ccCccccccccCCcccc-
Confidence 8999999999999999999999999999754311 11123333100 00011111111000000
Q ss_pred cccCCCCCCCCCCCCCCccCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCC
Q 007603 250 EFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYL 329 (596)
Q Consensus 250 ~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p 329 (596)
..+ ....+.+..+++.+|...++.|||++|..|+.++.++|+.|.+.....+ ++|+++..+.|
T Consensus 246 --------~~~------~~~~~~e~~~~~~~p~~~~~~v~g~~~~~i~~l~~~~~~~i~v~~~~~~---~~i~~s~~e~~ 308 (485)
T KOG2190|consen 246 --------PFG------GIVPEEELVFKLICPSDKVGSVIGKGGLVIRALRNETGASISVGDSRTD---RIVTISARENP 308 (485)
T ss_pred --------ccc------ccccchhhhhhhcCchhhceeeecCCCccchhhhhhcCCceEeccccCc---ceeeeccccCc
Confidence 000 0223466788999999999999999999999999999999999977554 89999999999
Q ss_pred CCCCchHHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccc
Q 007603 330 DTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLG 409 (596)
Q Consensus 330 ~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~ 409 (596)
++..+++++|+++++.++.+..... . ...++.+|+||++++||||||+|++|.+|++.|||.|+|...++.
T Consensus 309 ~~~~s~a~~a~~~~~~~~~~~~~~~------~-~~~v~~~l~vps~~igciiGk~G~~iseir~~tgA~I~I~~~~~~-- 379 (485)
T KOG2190|consen 309 EDRYSMAQEALLLVQPRISENAGDD------L-TQTVTQRLLVPSDLIGCIIGKGGAKISEIRQRTGASISILNKEEV-- 379 (485)
T ss_pred ccccccchhhhhhcccccccccccc------c-cceeeeeeccCccccceeecccccchHHHHHhcCCceEEcccccc--
Confidence 9999999999999999986643211 1 466899999999999999999999999999999999999998763
Q ss_pred cCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcccccc
Q 007603 410 CAAQNDVVIQISGEYKNVQNALSEVVGRLRHNLKSGE 446 (596)
Q Consensus 410 ~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~ 446 (596)
...+++.++|+|...+...|++++..++...-....
T Consensus 380 -~~~~e~~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~ 415 (485)
T KOG2190|consen 380 -SGVREALVQITGMLREDLLAQYLIRARLSAPKSSMG 415 (485)
T ss_pred -CCcceeEEEecchhHHHHhhhhhcccccccCccCCC
Confidence 257799999999999999999999888776554433
No 2
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=100.00 E-value=4e-42 Score=349.54 Aligned_cols=368 Identities=20% Similarity=0.312 Sum_probs=273.1
Q ss_pred CCCCCCcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeC-CCCCCCceEEEEccCcchhhhhhhccccccccCC
Q 007603 18 LNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGG 96 (596)
Q Consensus 18 ~~~~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~-~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~ 96 (596)
......+..+|+|||..++|+||||.|+|||.|.+.|.|+|+|.. ...|..||+|+|.+++|.
T Consensus 192 ~~~q~~D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrken~Gaaek~itvh~tpEg---------------- 255 (584)
T KOG2193|consen 192 HKQQLKDWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRKENAGAAEKIITVHSTPEG---------------- 255 (584)
T ss_pred ccccccCcceeeeeccceeEEEecCCCccccCcchhhhheeeeeecccCCcccCceEEecCccc----------------
Confidence 334466889999999999999999999999999999999999975 456889999999999987
Q ss_pred CccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCC-CCCCCCCC
Q 007603 97 EVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDD 175 (596)
Q Consensus 97 ~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~-p~~~~~~d 175 (596)
.+.|+..++.|+.+ ...+. .-..++.++++.++..||+||||.|++||+|+.+||++|.|++. .......|
T Consensus 256 -~s~Ac~~ILeimqk---EA~~~----k~~~e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis~lqels~ynpE 327 (584)
T KOG2193|consen 256 -TSKACKMILEIMQK---EAVDD----KVAEEIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITISKLQELSLYNPE 327 (584)
T ss_pred -hHHHHHHHHHHHHH---hhhcc----chhhhcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeeeehhhhcccCcc
Confidence 44555555555544 22211 12257899999999999999999999999999999999999986 33345679
Q ss_pred cEEEEeecHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCC---CCCCCCCCCccc
Q 007603 176 QLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPL---TGNPSDNASEFH 252 (596)
Q Consensus 176 RiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~---~~~~~~ya~~~~ 252 (596)
|+|++.|+.|+|.+|..+|..+|++....+-...... ..+|.+.++|.+ ++.....++.+.
T Consensus 328 RTItVkGsiEac~~AE~eImkKlre~yEnDl~a~s~q----------------~~l~P~l~~~~l~~f~ssS~~~~Ph~~ 391 (584)
T KOG2193|consen 328 RTITVKGSIEACVQAEAEIMKKLRECYENDLAAMSLQ----------------CHLPPGLNLPALGLFPSSSAVSPPHFP 391 (584)
T ss_pred ceEEecccHHHHHHHHHHHHHHHHHHHhhhHHHhhcc----------------CCCCcccCccccCCCCcccccCCCCCC
Confidence 9999999999999999999999998543221100000 001111111111 000000001011
Q ss_pred CCCCCCCCCCCCCCc-cCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCC-CCCCCccEEEEEecCCCC
Q 007603 253 SSSADADRDHPGLDK-KGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLD 330 (596)
Q Consensus 253 p~~~~~~r~~p~~~~-~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~~~er~v~IsG~e~p~ 330 (596)
|...... +.+.. ...++...++|+||...+|.|||++|.+||.|.+.+||.|+|..+ .++..+|.|+|+|..
T Consensus 392 Ps~v~~a---~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIappE~pdvseRMViItGpp--- 465 (584)
T KOG2193|consen 392 PSPVTFA---SPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIAPPEIPDVSERMVIITGPP--- 465 (584)
T ss_pred CCccccC---CCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeecCCCCCCcceeEEEecCCh---
Confidence 1111000 01110 122345578999999999999999999999999999999999965 667889999999973
Q ss_pred CCCchHHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCccccc
Q 007603 331 TRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGC 410 (596)
Q Consensus 331 ~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~ 410 (596)
.+...|.-+||.++.|..+- .+.......+.+.||...+|+||||||.+++++|+.|+|.+.|+... .|.
T Consensus 466 ---eaqfKAQgrifgKikEenf~-----~PkeevklethirVPs~~aGRvIGKGGktVnELQnlt~AeV~vPrdq-tpd- 535 (584)
T KOG2193|consen 466 ---EAQFKAQGRIFGKIKEENFF-----LPKEEVKLETHIRVPSSAAGRVIGKGGKTVNELQNLTSAEVVVPRDQ-TPD- 535 (584)
T ss_pred ---HHHHhhhhhhhhhhhhhccC-----CchhhheeeeeeeccchhhhhhhccccccHHHHhccccceEEccccC-CCC-
Confidence 23346777788888664321 12235668899999999999999999999999999999999998754 453
Q ss_pred CCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007603 411 AAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442 (596)
Q Consensus 411 ~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~ 442 (596)
..+..+|.|.|..-+.+.|+..|.+.|.+..
T Consensus 536 -End~vivriiGhfyatq~aQrki~~iv~qvk 566 (584)
T KOG2193|consen 536 -ENDQVIVRIIGHFYATQNAQRKIAHIVNQVK 566 (584)
T ss_pred -ccceeeeeeechhhcchHHHHHHHHHHHHHH
Confidence 5667899999999999999999999888744
No 3
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=100.00 E-value=2.1e-40 Score=352.97 Aligned_cols=338 Identities=22% Similarity=0.304 Sum_probs=261.3
Q ss_pred CcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHH
Q 007603 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (596)
Q Consensus 23 ~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~ 102 (596)
..++-+.-||..++|.||||+|+.|..|+.++||+|.+.....+..+|-+.+.|..++++. |.
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~~s~~~~r~~~~~G~pe~v~~-----------------aK 114 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAADPSGIGYRSVDLTGSPENVEV-----------------AK 114 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCCCCCcccccccccCCcccHHH-----------------HH
Confidence 4567788899999999999999999999999999999877666778999999999988654 33
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEee
Q 007603 103 EAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG 182 (596)
Q Consensus 103 ~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G 182 (596)
..+..+..+..... ... .......++..++||++.+|.||||+|++||.|++++||++.+.++.......++.+.|+|
T Consensus 115 ~li~evv~r~~~~~-~~~-~~q~~~~ttqeI~IPa~k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritG 192 (600)
T KOG1676|consen 115 QLIGEVVSRGRPPG-GFP-DNQGSVETTQEILIPANKCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITG 192 (600)
T ss_pred HhhhhhhhccCCCC-Ccc-ccCCccceeeeeccCccceeeEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecC
Confidence 33444444433110 000 1122457899999999999999999999999999999999999987333344789999999
Q ss_pred cHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCC
Q 007603 183 ATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDH 262 (596)
Q Consensus 183 ~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~ 262 (596)
++++|+.|..+|.++|++... .... ....++. |
T Consensus 193 dp~~ve~a~~lV~dil~e~~~---~~~g--------------------------------~~~~~g~----------~-- 225 (600)
T KOG1676|consen 193 DPDKVEQAKQLVADILREEDD---EVPG--------------------------------SGGHAGV----------R-- 225 (600)
T ss_pred CHHHHHHHHHHHHHHHHhccc---CCCc--------------------------------cccccCc----------C--
Confidence 999999999999999986211 0000 0000000 0
Q ss_pred CCCCccCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCC-CCCCCccEEEEEecCCCCCCCchHHHHHH
Q 007603 263 PGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAP-LTKSGERVVTISALEYLDTRHSPVQNAAV 341 (596)
Q Consensus 263 p~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~-~~~~~er~v~IsG~e~p~~~~~~a~~Av~ 341 (596)
.-...+++|.||...||.||||+|++||+|+.+||++|+|..+ .+.+.+|++.|.|+. ..+..|..
T Consensus 226 -------~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~p~speR~~~IiG~~------d~ie~Aa~ 292 (600)
T KOG1676|consen 226 -------GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDDPSSPERPAQIIGTV------DQIEHAAE 292 (600)
T ss_pred -------ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCCCCCccceeeeecCH------HHHHHHHH
Confidence 0123388999999999999999999999999999999999865 447889999999984 55666776
Q ss_pred HHHhhhhhccccCCCCCCCCCCCc--eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEE
Q 007603 342 LVFARSVEVEGQQGFSSGENKGDA--VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ 419 (596)
Q Consensus 342 ~i~~~i~e~~~~~g~~~g~~~~~~--~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~ 419 (596)
+|.+.+.+.....+..-+. .... ....+.||++.||.||||+|++||.|.++|||++.+.+. |.....++++++
T Consensus 293 lI~eii~~~~~~~~~~~~~-G~P~~~~~fy~~VPa~KcGLvIGrGGEtIK~in~qSGA~~el~r~---~p~~~~~ektf~ 368 (600)
T KOG1676|consen 293 LINEIIAEAEAGAGGGMGG-GAPGLVAQFYMKVPADKCGLVIGRGGETIKQINQQSGARCELSRQ---PPNGNPKEKTFV 368 (600)
T ss_pred HHHHHHHHHhccCCCCcCC-CCccceeeEEEeccccccccccCCCccchhhhcccCCccccccCC---CCCCCccceEEE
Confidence 7666665443222111110 1112 288999999999999999999999999999999999875 233678899999
Q ss_pred EcCCHHHHHHHHHHHHHHHhhccc
Q 007603 420 ISGEYKNVQNALSEVVGRLRHNLK 443 (596)
Q Consensus 420 I~G~~~~V~~A~~~I~~~Lr~~~~ 443 (596)
|+|+..+|..|+.||..++-+...
T Consensus 369 IrG~~~QIdhAk~LIr~kvg~~~~ 392 (600)
T KOG1676|consen 369 IRGDKRQIDHAKQLIRDKVGDIAP 392 (600)
T ss_pred EecCcccchHHHHHHHHHhcccCC
Confidence 999999999999999999987443
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=5.9e-32 Score=261.55 Aligned_cols=333 Identities=17% Similarity=0.266 Sum_probs=208.5
Q ss_pred CCCCcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCcc
Q 007603 20 LPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVS 99 (596)
Q Consensus 20 ~~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~ 99 (596)
.....+.+|||+.++.+|+||||+|+|||.|+.+.++.|.|.+. ..+|||++|+...+-
T Consensus 43 ~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds--~~peri~tisad~~t------------------- 101 (390)
T KOG2192|consen 43 FKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDS--SGPERILTISADIET------------------- 101 (390)
T ss_pred hhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCC--CCCceeEEEeccHHH-------------------
Confidence 34457999999999999999999999999999999999999887 568999999976543
Q ss_pred HHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEE
Q 007603 100 STQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQ 179 (596)
Q Consensus 100 ~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~ 179 (596)
+..|+.++.....+. -...+.+.+||||+.+++|.|||++|++||+|++++.|++.|... -|+.++||+|.
T Consensus 102 -----i~~ilk~iip~lee~---f~~~~pce~rllihqs~ag~iigrngskikelrekcsarlkift~-c~p~stdrv~l 172 (390)
T KOG2192|consen 102 -----IGEILKKIIPTLEEG---FQLPSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKIFTE-CCPHSTDRVVL 172 (390)
T ss_pred -----HHHHHHHHhhhhhhC---CCCCCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhhhhc-cCCCCcceEEE
Confidence 334444433322111 112337899999999999999999999999999999999999984 78999999999
Q ss_pred EeecHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCC------CCCCCCcCCCcCCCCCCCCCCCCCCCcccC
Q 007603 180 ITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNS------SDPHREFFPHLSLVPPLTGNPSDNASEFHS 253 (596)
Q Consensus 180 I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~------~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p 253 (596)
|.|.+..|..++..|.+.|.+.+.+... +|+...+++.. .-+..+....+..+|+.++...
T Consensus 173 ~~g~~k~v~~~i~~il~~i~e~pikgsa-----~py~p~fyd~t~dyggf~M~f~d~pg~pgpapqrggqgp-------- 239 (390)
T KOG2192|consen 173 IGGKPKRVVECIKIILDLISESPIKGSA-----QPYDPNFYDETYDYGGFTMMFDDRPGRPGPAPQRGGQGP-------- 239 (390)
T ss_pred ecCCcchHHHHHHHHHHHhhcCCcCCcC-----CcCCccccCcccccCCceeecCCCCCCCCCCCCCCCCCC--------
Confidence 9999999999999999999997765442 22222222111 0000000000011111110000
Q ss_pred CCCCCCCCCCCCCccCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCC
Q 007603 254 SSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRH 333 (596)
Q Consensus 254 ~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~ 333 (596)
.....+ . +.-+-++|.-=. .+.-.+.|...... .. +-...
T Consensus 240 --------------p~~~~s----------d-lmay~r~GrpG~----rydg~vdFs~detw---------~s--aidtw 279 (390)
T KOG2192|consen 240 --------------PPPRGS----------D-LMAYDRRGRPGD----RYDGMVDFSADETW---------PS--AIDTW 279 (390)
T ss_pred --------------CCCCcc----------c-cceeccCCCCCc----cccccccccccccC---------CC--cCCCc
Confidence 000000 0 000001110000 00000111110000 00 00000
Q ss_pred chH--HHHHHHHHhhhhhccccCCCCC-CCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCccccc
Q 007603 334 SPV--QNAAVLVFARSVEVEGQQGFSS-GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGC 410 (596)
Q Consensus 334 ~~a--~~Av~~i~~~i~e~~~~~g~~~-g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~ 410 (596)
++. +-|-.--...--+.....++.+ +.-.....|+.+.||++.-|.||||+|+.|++|++++||.|+|....
T Consensus 280 ~~SewqmaYePQgGs~ydysyAG~~GsYGdlGGPitTaQvtip~dlggsiigkggqri~~ir~esGA~Ikidepl----- 354 (390)
T KOG2192|consen 280 SPSEWQMAYEPQGGSGYDYSYAGGYGSYGDLGGPITTAQVTIPKDLGGSIIGKGGQRIKQIRHESGASIKIDEPL----- 354 (390)
T ss_pred CccccccccCCCCCCCCCccccccccccCCCCCceeeeeEecccccCcceecccchhhhhhhhccCceEEecCcC-----
Confidence 000 0000000000000000000000 11125678999999999999999999999999999999999997643
Q ss_pred CCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007603 411 AAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 411 ~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (596)
.++.+|+++|+|+.++++.|++|+...++.
T Consensus 355 eGsedrIitItGTqdQIqnAQYLlQn~Vkq 384 (390)
T KOG2192|consen 355 EGSEDRIITITGTQDQIQNAQYLLQNSVKQ 384 (390)
T ss_pred CCCCceEEEEeccHHHHhhHHHHHHHHHHh
Confidence 378899999999999999999999998885
No 5
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=99.96 E-value=8.5e-29 Score=252.57 Aligned_cols=260 Identities=18% Similarity=0.292 Sum_probs=202.3
Q ss_pred ceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCCC
Q 007603 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (596)
Q Consensus 128 ~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~~ 207 (596)
+..+|+|||..++|.||||.|++||.|...|-|+|.|... ...+..|++|+|.|++|...+|+.+|.++++.....+
T Consensus 198 D~PlR~lVptqyvgaIIGkeG~TIknItkqTqsriD~hrk-en~Gaaek~itvh~tpEg~s~Ac~~ILeimqkEA~~~-- 274 (584)
T KOG2193|consen 198 DWPLRLLVPTQYVGAIIGKEGATIKNITKQTQSRIDVHRK-ENAGAAEKIITVHSTPEGTSKACKMILEIMQKEAVDD-- 274 (584)
T ss_pred CcceeeeeccceeEEEecCCCccccCcchhhhheeeeeec-ccCCcccCceEEecCccchHHHHHHHHHHHHHhhhcc--
Confidence 4679999999999999999999999999999999999986 5568899999999999999999999999997632111
Q ss_pred CcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccCCCcceEEEEEeccccccc
Q 007603 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (596)
Q Consensus 208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~ 287 (596)
....++.++++..+.+||+
T Consensus 275 -------------------------------------------------------------k~~~e~pLk~lAHN~lvGR 293 (584)
T KOG2193|consen 275 -------------------------------------------------------------KVAEEIPLKILAHNNLVGR 293 (584)
T ss_pred -------------------------------------------------------------chhhhcchhhhhhcchhhh
Confidence 1235678899999999999
Q ss_pred cccccchhhhhhhhccCeeEEEeCC---CCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhh---cc---------c
Q 007603 288 IIGKRGAIVRSLQNASGALISFAAP---LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVE---VE---------G 352 (596)
Q Consensus 288 IIGk~G~~Ik~I~~~tGa~I~i~~~---~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e---~~---------~ 352 (596)
+|||.|.+||+|+.+||++|.|... ..-..||+|++.|+- .....|-..|..++.+ ++ .
T Consensus 294 LIGKeGrnlKkIeq~TgTkITis~lqels~ynpERTItVkGsi------Eac~~AE~eImkKlre~yEnDl~a~s~q~~l 367 (584)
T KOG2193|consen 294 LIGKEGRNLKKIEQDTGTKITISKLQELSLYNPERTITVKGSI------EACVQAEAEIMKKLRECYENDLAAMSLQCHL 367 (584)
T ss_pred hhhhccccHHHHHhhcCCceeeeehhhhcccCccceEEecccH------HHHHHHHHHHHHHHHHHHhhhHHHhhccCCC
Confidence 9999999999999999999999853 334569999999972 3333444444444332 11 1
Q ss_pred cCCC-------------------CCCC-----------CCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEe
Q 007603 353 QQGF-------------------SSGE-----------NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (596)
Q Consensus 353 ~~g~-------------------~~g~-----------~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~ 402 (596)
..++ ++.. ........+|.||...+|.|||++|.+||.|.+.+||.|+|.
T Consensus 368 ~P~l~~~~l~~f~ssS~~~~Ph~~Ps~v~~a~p~~~~hq~pe~e~V~~fiP~~~vGAiIGkkG~hIKql~RfagASiKIa 447 (584)
T KOG2193|consen 368 PPGLNLPALGLFPSSSAVSPPHFPPSPVTFASPYPLFHQNPEQEQVRMFIPAQAVGAIIGKKGQHIKQLSRFAGASIKIA 447 (584)
T ss_pred CcccCccccCCCCcccccCCCCCCCCccccCCCchhhhcCcchhheeeeccHHHHHHHHhhcchhHHHHHHhccceeeec
Confidence 1111 0100 012456789999999999999999999999999999999998
Q ss_pred CCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh--cccccc-ccCCCCCCCCCCCCC
Q 007603 403 GGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH--NLKSGE-ILNEARPRSPSGRVG 461 (596)
Q Consensus 403 ~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~--~~~~~~-~~~~~~~r~~~~~~g 461 (596)
+.+- .+..+|+|+|+|.+++..+|+..|..+|.+ |+...+ +.-..+-|.|...+|
T Consensus 448 ppE~----pdvseRMViItGppeaqfKAQgrifgKikEenf~~PkeevklethirVPs~~aG 505 (584)
T KOG2193|consen 448 PPEI----PDVSERMVIITGPPEAQFKAQGRIFGKIKEENFFLPKEEVKLETHIRVPSSAAG 505 (584)
T ss_pred CCCC----CCcceeEEEecCChHHHHhhhhhhhhhhhhhccCCchhhheeeeeeeccchhhh
Confidence 8653 357899999999999999999999999985 333333 333344555544333
No 6
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=99.96 E-value=4e-28 Score=259.31 Aligned_cols=245 Identities=20% Similarity=0.304 Sum_probs=193.9
Q ss_pred CceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCC
Q 007603 127 DVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (596)
Q Consensus 127 ~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~ 206 (596)
..++.+.-||..++|.||||+|+.|..|+.+|||+|+|... ......|.|.++|.+++|+.|+.+|.+++....
T Consensus 52 ~~~~~~~~VPd~~VglvIGrgG~qI~~iqq~SgCrvq~~~~--~s~~~~r~~~~~G~pe~v~~aK~li~evv~r~~---- 125 (600)
T KOG1676|consen 52 TVQTERYKVPDEAVGLVIGRGGSQIQAIQQKSGCRVQIAAD--PSGIGYRSVDLTGSPENVEVAKQLIGEVVSRGR---- 125 (600)
T ss_pred cccccccCCCchhceeEeeccHHHhhhhhhhcCCccccCCC--CCCcccccccccCCcccHHHHHHhhhhhhhccC----
Confidence 46788899999999999999999999999999999998774 234578999999999999999999999986521
Q ss_pred CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccCCCcceEEEEEecccccc
Q 007603 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (596)
Q Consensus 207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg 286 (596)
.+. .+++ .....+++.+|.||.+++|
T Consensus 126 ~~~--------------------~~~~----------------------------------~q~~~~ttqeI~IPa~k~G 151 (600)
T KOG1676|consen 126 PPG--------------------GFPD----------------------------------NQGSVETTQEILIPANKCG 151 (600)
T ss_pred CCC--------------------Cccc----------------------------------cCCccceeeeeccCcccee
Confidence 000 0000 1113567999999999999
Q ss_pred ccccccchhhhhhhhccCeeEEEeCC--CCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhcc---ccCCCCCCCC
Q 007603 287 GIIGKRGAIVRSLQNASGALISFAAP--LTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE---GQQGFSSGEN 361 (596)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~--~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~---~~~g~~~g~~ 361 (596)
.||||+|++||.|++.+||++.+..+ ......+.+.|+|.. ..+..|-.++++.+.+.. +..+...+..
T Consensus 152 lIIGKgGETikqlqe~sg~k~i~iqd~~~~~~~~KplritGdp------~~ve~a~~lV~dil~e~~~~~~g~~~~~g~~ 225 (600)
T KOG1676|consen 152 LIIGKGGETIKQLQEQSGVKMILVQDGSIATGADKPLRITGDP------DKVEQAKQLVADILREEDDEVPGSGGHAGVR 225 (600)
T ss_pred eEeccCccHHHHHHhhcCCceEEEecCCcCCCCCCceeecCCH------HHHHHHHHHHHHHHHhcccCCCccccccCcC
Confidence 99999999999999999999887643 223367889999973 445566666666665321 1111111112
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007603 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (596)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (596)
.....+.+|.||...||.||||+|++||+|+.+|||+|+|.+.++ | .+.+|.+.|.|+.++|+.|.++|.++|++.
T Consensus 226 ~g~~~~~~V~VPr~~VG~IIGkgGE~IKklq~etG~KIQfkpDd~-p---~speR~~~IiG~~d~ie~Aa~lI~eii~~~ 301 (600)
T KOG1676|consen 226 GGGSATREVKVPRSKVGIIIGKGGEMIKKLQNETGAKIQFKPDDD-P---SSPERPAQIIGTVDQIEHAAELINEIIAEA 301 (600)
T ss_pred ccccceeEEeccccceeeEEecCchHHHHHhhccCceeEeecCCC-C---CCccceeeeecCHHHHHHHHHHHHHHHHHH
Confidence 234559999999999999999999999999999999999988666 3 578999999999999999999999999863
No 7
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.94 E-value=3.1e-26 Score=228.13 Aligned_cols=239 Identities=20% Similarity=0.300 Sum_probs=173.1
Q ss_pred CCCCCcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEe---CCCCCCCceEEEEccCcchhhhhhhccccccccC
Q 007603 19 NLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE---GGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG 95 (596)
Q Consensus 19 ~~~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~---~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~ 95 (596)
..-++.+++|||||+..+|.||||+|++|.+|+++|||+|+++ |++|++.||||+|.|+.+++.
T Consensus 33 ~ge~~~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~------------- 99 (402)
T KOG2191|consen 33 TGEDGQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALN------------- 99 (402)
T ss_pred CCCCCceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHH-------------
Confidence 3344459999999999999999999999999999999999996 578999999999999876531
Q ss_pred CCccHHHHHHHHHHHHHHhhhhccCC------CCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCC-C
Q 007603 96 GEVSSTQEAVIRVFERMWEVEAEVEG------DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-P 168 (596)
Q Consensus 96 ~~~~~A~~Al~~i~~~i~~~~~~~~~------~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~-p 168 (596)
.-+..|.++|.+.....+. ....++.-.++++||+..+|.||||+|.+||.|++++||.|+|++. |
T Consensus 100 -------av~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~iqisPqkp 172 (402)
T KOG2191|consen 100 -------AVHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAWIQISPQKP 172 (402)
T ss_pred -------HHHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcceEecccCC
Confidence 1233455555554433322 1223445679999999999999999999999999999999999953 5
Q ss_pred CCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCC
Q 007603 169 ACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNA 248 (596)
Q Consensus 169 ~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya 248 (596)
..-...||+|+++|++++..+|+.+|.++|.+++....... .++.... +....|+
T Consensus 173 t~~sLqervvt~sge~e~~~~A~~~IL~Ki~eDpqs~scln---~sya~vs----------------------GpvaNsn 227 (402)
T KOG2191|consen 173 TGISLQERVVTVSGEPEQNMKAVSLILQKIQEDPQSGSCLN---ISYANVS----------------------GPVANSN 227 (402)
T ss_pred CCccceeEEEEecCCHHHHHHHHHHHHHHhhcCCcccceec---cchhccc----------------------CcccccC
Confidence 55567899999999999999999999999999765433211 0000000 0011111
Q ss_pred CcccCCCCCCCCCCCCCCccCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeC
Q 007603 249 SEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAA 311 (596)
Q Consensus 249 ~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~ 311 (596)
+...|+.... ...+...+.-.-++....|..-|.+|.+.-.|..-+|+.+.+..
T Consensus 228 PtGspya~~~---------~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq 281 (402)
T KOG2191|consen 228 PTGSPYAYQA---------HVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQ 281 (402)
T ss_pred CCCCCCCCCC---------ccccccchhhccccccccccccccccccceeeecccccceeecc
Confidence 1111111100 01112223335588899999999999999999999999888875
No 8
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.90 E-value=5.7e-23 Score=204.97 Aligned_cols=250 Identities=21% Similarity=0.289 Sum_probs=196.3
Q ss_pred ceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCC-CCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCC
Q 007603 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP-PACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEK 206 (596)
Q Consensus 128 ~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~-p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~ 206 (596)
.+.+|+|||+..+|.||||+|++|.+++.+|||+|++++. ..+|+++||+|.|+|+.++|......|.++|++.+....
T Consensus 38 ~y~ikvLips~AaGsIIGKGG~ti~~lqk~tgariklSks~dfyPGTTeRvcli~Gt~eai~av~efI~dKire~p~~~~ 117 (402)
T KOG2191|consen 38 QYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGARIKLSKSKDFYPGTTERVCLIQGTVEALNAVHEFIADKIREKPQAVA 117 (402)
T ss_pred ceEEEEEeecccccceeccchHHHHHHHhccCcEEEeccccccCCCccceEEEEeccHHHHHHHHHHHHHHHHHhHHhhc
Confidence 4899999999999999999999999999999999999988 889999999999999999999999999999998543221
Q ss_pred CCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccCCCcceEEEEEecccccc
Q 007603 207 SPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTAS 286 (596)
Q Consensus 207 ~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg 286 (596)
.+.... ++......-.+++++|+..+|
T Consensus 118 k~v~~~-----------------------------------------------------~pqt~~r~kqikivvPNstag 144 (402)
T KOG2191|consen 118 KPVDIL-----------------------------------------------------QPQTPDRIKQIKIVVPNSTAG 144 (402)
T ss_pred CCcccc-----------------------------------------------------CCCCccccceeEEeccCCccc
Confidence 110000 000011223588999999999
Q ss_pred ccccccchhhhhhhhccCeeEEEeCCC---CCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccc-------cC--
Q 007603 287 GIIGKRGAIVRSLQNASGALISFAAPL---TKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG-------QQ-- 354 (596)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~---~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~-------~~-- 354 (596)
.||||+|.+||.|++++||+|+|.+.+ ..-.+|+||++|.. .....|+.+|+.++.++.- ..
T Consensus 145 ~iigkggAtiK~~~Eqsga~iqisPqkpt~~sLqervvt~sge~------e~~~~A~~~IL~Ki~eDpqs~scln~sya~ 218 (402)
T KOG2191|consen 145 MIIGKGGATIKAIQEQSGAWIQISPQKPTGISLQERVVTVSGEP------EQNMKAVSLILQKIQEDPQSGSCLNISYAN 218 (402)
T ss_pred ceecCCcchHHHHHHhhCcceEecccCCCCccceeEEEEecCCH------HHHHHHHHHHHHHhhcCCcccceeccchhc
Confidence 999999999999999999999999532 23468999999984 5567899999999876521 00
Q ss_pred --C----CCC-C-------CCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEE
Q 007603 355 --G----FSS-G-------ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQI 420 (596)
Q Consensus 355 --g----~~~-g-------~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I 420 (596)
| +.| | ...+...+....|+....|-.-|.+|..+-.+...+|+.+.++...+.- .+...+ +-+
T Consensus 219 vsGpvaNsnPtGspya~~~~~~~astas~~sva~~~iG~a~gaG~~~~a~l~~~~G~l~~itq~l~~m--~g~gy~-~n~ 295 (402)
T KOG2191|consen 219 VSGPVANSNPTGSPYAYQAHVLPASTASTISVAAGLIGGANGAGGAFGAALSGFTGALIAITQALNTM--AGYGYN-TNI 295 (402)
T ss_pred ccCcccccCCCCCCCCCCCccccccchhhccccccccccccccccccceeeecccccceeeccccccc--cccccc-ccc
Confidence 0 111 0 1124556777889999999999999999999999999999998866522 233334 888
Q ss_pred cCCHHHHHHHHHHHHHHHh
Q 007603 421 SGEYKNVQNALSEVVGRLR 439 (596)
Q Consensus 421 ~G~~~~V~~A~~~I~~~Lr 439 (596)
.|...+++.|-.+|.....
T Consensus 296 ~g~~ls~~aa~g~L~~~~~ 314 (402)
T KOG2191|consen 296 LGLGLSILAAEGVLAAKVA 314 (402)
T ss_pred cchhhhhhhhhhHHHHhhc
Confidence 9999999999888876543
No 9
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=99.85 E-value=6.5e-20 Score=199.42 Aligned_cols=165 Identities=27% Similarity=0.400 Sum_probs=139.0
Q ss_pred ceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccc
Q 007603 273 EVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEG 352 (596)
Q Consensus 273 ~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~ 352 (596)
..++||+|+...+|.||||+|..||+|+.++.++|+|.+...++.+|+|+|+|+.... ..+++++|+.+.++++.....
T Consensus 42 t~~~RlL~~~kevG~IIGk~G~~vkkir~~t~s~i~i~~~~~~c~eRIiti~g~~~~~-~~~~~~~al~ka~~~iv~~~~ 120 (485)
T KOG2190|consen 42 TLTYRLLCHVKEVGSIIGKKGDIVKKIRKETESKIRVNESLPGCPERIITITGNRVEL-NLSPATDALFKAFDMIVFKLE 120 (485)
T ss_pred cceEEEEeccccceeEEccCcHHHHHHhhcccccceeecCCCCCCcceEEEecccccc-cCCchHHHHHHHHHHHhhccc
Confidence 3359999999999999999999999999999999999998899999999999953222 567889999999998865311
Q ss_pred ---cCCCCCC-CCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHH
Q 007603 353 ---QQGFSSG-ENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQ 428 (596)
Q Consensus 353 ---~~g~~~g-~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~ 428 (596)
....+.+ ......++.+|+||.+++|+||||+|+.||+|++.|||+|+|.+. .+|. .++|.|+|.|.+++|.
T Consensus 121 ~d~~~~~d~~~~~~~~~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~-~lP~---ster~V~IsG~~~av~ 196 (485)
T KOG2190|consen 121 EDDEAAEDNGEDASGPEVTCRLLVPSSQVGSLIGKGGSLIKEIREETGAKIRVSSD-MLPN---STERAVTISGEPDAVK 196 (485)
T ss_pred ccccccccCCccccCCceEEEEEechhheeeeeccCcHHHHHHHHhcCceEEecCC-CCCc---ccceeEEEcCchHHHH
Confidence 1111111 112235899999999999999999999999999999999999986 5665 6788899999999999
Q ss_pred HHHHHHHHHHhhcc
Q 007603 429 NALSEVVGRLRHNL 442 (596)
Q Consensus 429 ~A~~~I~~~Lr~~~ 442 (596)
+|+..|..+|++++
T Consensus 197 ~al~~Is~~L~~~~ 210 (485)
T KOG2190|consen 197 KALVQISSRLLENP 210 (485)
T ss_pred HHHHHHHHHHHhcC
Confidence 99999999999975
No 10
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=99.61 E-value=2.2e-15 Score=146.84 Aligned_cols=147 Identities=21% Similarity=0.327 Sum_probs=125.4
Q ss_pred ceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCCC
Q 007603 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKS 207 (596)
Q Consensus 128 ~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~~ 207 (596)
.+.+|||+.++.+|.||||+|++||+|+.+++|.|+|.. ....+|+++|+.+.+.|-.-++.|.-.|++..
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpd----s~~peri~tisad~~ti~~ilk~iip~lee~f----- 117 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPD----SSGPERILTISADIETIGEILKKIIPTLEEGF----- 117 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccC----CCCCceeEEEeccHHHHHHHHHHHhhhhhhCC-----
Confidence 689999999999999999999999999999999999976 35689999999999999999999999998731
Q ss_pred CcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccCCCcceEEEEEeccccccc
Q 007603 208 PICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASG 287 (596)
Q Consensus 208 ~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~ 287 (596)
.+...+.++|+|..+++|.
T Consensus 118 -------------------------------------------------------------~~~~pce~rllihqs~ag~ 136 (390)
T KOG2192|consen 118 -------------------------------------------------------------QLPSPCELRLLIHQSLAGG 136 (390)
T ss_pred -------------------------------------------------------------CCCCchhhhhhhhhhhccc
Confidence 1223468899999999999
Q ss_pred cccccchhhhhhhhccCeeEEEe-CCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhc
Q 007603 288 IIGKRGAIVRSLQNASGALISFA-APLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV 350 (596)
Q Consensus 288 IIGk~G~~Ik~I~~~tGa~I~i~-~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~ 350 (596)
|||++|++||++++++.|+.+|. ...+.+++|+|.|.|.. ..+.+.+..+.+.+.+.
T Consensus 137 iigrngskikelrekcsarlkift~c~p~stdrv~l~~g~~------k~v~~~i~~il~~i~e~ 194 (390)
T KOG2192|consen 137 IIGRNGSKIKELREKCSARLKIFTECCPHSTDRVVLIGGKP------KRVVECIKIILDLISES 194 (390)
T ss_pred eecccchhHHHHHHhhhhhhhhhhccCCCCcceEEEecCCc------chHHHHHHHHHHHhhcC
Confidence 99999999999999999999988 45889999999999973 33445555556666554
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=99.45 E-value=2.3e-13 Score=130.21 Aligned_cols=138 Identities=17% Similarity=0.192 Sum_probs=95.3
Q ss_pred EEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEE---ccCcchhhhhhhccccccccCCCccHHHHHH
Q 007603 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILV---VGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (596)
Q Consensus 29 ilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I---~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al 105 (596)
+-||.+++|.|||++|++|++|+++|||+|++.+. +..|.| +++++.+ ..|.+.+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t~d~~~i-----------------~kA~~~I 59 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEEDEDPLAV-----------------MKAREVV 59 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCCCCHHHH-----------------HHHHHHH
Confidence 45799999999999999999999999999999753 245777 3444332 2233332
Q ss_pred HHHHHHHHhhhhccCCCCCCCCceEEEE-Eecc---------ceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCC
Q 007603 106 IRVFERMWEVEAEVEGDGDGDDVAYCGL-LANT---------TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (596)
Q Consensus 106 ~~i~~~i~~~~~~~~~~~~~~~~vt~rl-lVp~---------~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~d 175 (596)
..+..- ...+. .-.--...+++++ -|+. ..+|.|||++|++++.|++.|||+|.|. +
T Consensus 60 ~~i~~g---f~~e~-A~~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~---------~ 126 (172)
T TIGR03665 60 KAIGRG---FSPEK-ALKLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVY---------G 126 (172)
T ss_pred HHHHcC---CCHHH-HHHhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEc---------C
Confidence 222110 00000 0000001223322 2222 3689999999999999999999999994 3
Q ss_pred cEEEEeecHHHHHHHHHHHHHHHhcc
Q 007603 176 QLIQITGATLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 176 RiV~I~G~~e~V~~A~~~I~~~L~e~ 201 (596)
+.|.|.|+++++..|..+|.+++.+.
T Consensus 127 ~~v~i~G~~~~~~~A~~~i~~li~~~ 152 (172)
T TIGR03665 127 KTVGIIGDPEQVQIAREAIEMLIEGA 152 (172)
T ss_pred CEEEEECCHHHHHHHHHHHHHHHcCC
Confidence 67999999999999999999999663
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=99.43 E-value=5.9e-13 Score=127.44 Aligned_cols=141 Identities=19% Similarity=0.221 Sum_probs=97.3
Q ss_pred EEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCC
Q 007603 278 MLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFS 357 (596)
Q Consensus 278 l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~ 357 (596)
+.||.+.+|.|||++|++|+.|+++||++|.+++. +..|.|.... .+ ...+..|...+........++..+
T Consensus 2 i~Ip~~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----~g~V~I~~~t-~d--~~~i~kA~~~I~~i~~gf~~e~A~- 72 (172)
T TIGR03665 2 VKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSE-----TGEVKIEEED-ED--PLAVMKAREVVKAIGRGFSPEKAL- 72 (172)
T ss_pred ccCCHHHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----CceEEEecCC-CC--HHHHHHHHHHHHHHHcCCCHHHHH-
Confidence 56899999999999999999999999999999953 2468884110 11 133445544443322110000000
Q ss_pred CCCCCCCceEEEEEecc---------ccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHH
Q 007603 358 SGENKGDAVAVSILVGA---------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQ 428 (596)
Q Consensus 358 ~g~~~~~~~t~~l~VP~---------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~ 428 (596)
..-.....-.-+.|+. ..+|+|||++|++++.|++.|||+|.|.. ..|.|.|++++++
T Consensus 73 -~l~gd~y~~~Vi~I~~~~~~~~~~~~~~griIG~~G~t~~~ie~~t~~~i~i~~------------~~v~i~G~~~~~~ 139 (172)
T TIGR03665 73 -KLLDDDYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYG------------KTVGIIGDPEQVQ 139 (172)
T ss_pred -HhcCCcceEEEEEhhhccCCHHHHHHHHhhhcCCCcHHHHHHHHHHCCeEEEcC------------CEEEEECCHHHHH
Confidence 0000111222234443 47999999999999999999999999952 6799999999999
Q ss_pred HHHHHHHHHHhh
Q 007603 429 NALSEVVGRLRH 440 (596)
Q Consensus 429 ~A~~~I~~~Lr~ 440 (596)
.|..+|...|..
T Consensus 140 ~A~~~i~~li~~ 151 (172)
T TIGR03665 140 IAREAIEMLIEG 151 (172)
T ss_pred HHHHHHHHHHcC
Confidence 999999987754
No 13
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.43 E-value=8e-13 Score=127.38 Aligned_cols=142 Identities=16% Similarity=0.214 Sum_probs=97.6
Q ss_pred EEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEc----cCcchhhhhhhccccccccCCCccH
Q 007603 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVV----GSGSIDRRIMFCENDVVVEGGEVSS 100 (596)
Q Consensus 25 ~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~----G~~e~~~~a~~~~~~~~~e~~~~~~ 100 (596)
+...+-||.+++|.|||++|++|+.|+++|||+|.+.+. +..|.|. ++++.. ..
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d~~~i-----------------~k 60 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGEDPLAV-----------------LK 60 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCCHHHH-----------------HH
Confidence 467788999999999999999999999999999999753 2456664 333332 22
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEE-----ec-----cceeeeeeecCchhhhhhccccccEEEecCCCCC
Q 007603 101 TQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLL-----AN-----TTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPAC 170 (596)
Q Consensus 101 A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rll-----Vp-----~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~ 170 (596)
|++.+..+..-. +.+... ..-...+..++. .+ ...+|.|||++|++++.|++.|||+|.|..
T Consensus 61 A~~~I~ai~~gf-~~e~A~---~l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~---- 132 (180)
T PRK13763 61 ARDIVKAIGRGF-SPEKAL---RLLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG---- 132 (180)
T ss_pred HHHHHHHHhcCC-CHHHHH---HHhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC----
Confidence 333322222100 000000 000012222221 11 136899999999999999999999999954
Q ss_pred CCCCCcEEEEeecHHHHHHHHHHHHHHHhcc
Q 007603 171 AAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 171 ~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~ 201 (596)
+.|.|.|+++++..|...|..++++.
T Consensus 133 -----~~v~i~G~~~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 133 -----KTVAIIGDPEQVEIAREAIEMLIEGA 158 (180)
T ss_pred -----CEEEEEeCHHHHHHHHHHHHHHHcCC
Confidence 45899999999999999999999663
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=99.38 E-value=3.3e-12 Score=123.08 Aligned_cols=147 Identities=19% Similarity=0.220 Sum_probs=99.3
Q ss_pred eEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhcccc
Q 007603 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ 353 (596)
Q Consensus 274 ~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~ 353 (596)
+...+.||.+.++.|||++|.+|+.|+++||++|++.+. +..|.|.-...++ ...+..|...+..-.....++
T Consensus 3 ~~~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----~g~V~I~~~~~~d--~~~i~kA~~~I~ai~~gf~~e 75 (180)
T PRK13763 3 MMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSE-----TGEVIIEPTDGED--PLAVLKARDIVKAIGRGFSPE 75 (180)
T ss_pred ceEEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECC-----CCeEEEEeCCCCC--HHHHHHHHHHHHHHhcCCCHH
Confidence 356788999999999999999999999999999999953 2567776111011 133444544443322210000
Q ss_pred CCCCCCCCCCCceEEEEEec---------cccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCH
Q 007603 354 QGFSSGENKGDAVAVSILVG---------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEY 424 (596)
Q Consensus 354 ~g~~~g~~~~~~~t~~l~VP---------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~ 424 (596)
..+- .-.....-..+.|. ...+|+|||++|++++.|++.|||+|.|.. ..|.|.|++
T Consensus 76 ~A~~--l~gd~y~~~Vi~i~~~~~~~~~~~r~~griIG~~G~~~k~ie~~t~~~i~i~~------------~~v~i~G~~ 141 (180)
T PRK13763 76 KALR--LLDDDYVLEVIDLSDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYG------------KTVAIIGDP 141 (180)
T ss_pred HHHH--HhCCCceEEEEEhhhccCChhHHHHHhhheeCCCcHHHHHHHHHHCcEEEEcC------------CEEEEEeCH
Confidence 0000 00001111111111 147999999999999999999999999963 349999999
Q ss_pred HHHHHHHHHHHHHHhhc
Q 007603 425 KNVQNALSEVVGRLRHN 441 (596)
Q Consensus 425 ~~V~~A~~~I~~~Lr~~ 441 (596)
++++.|...|...++.+
T Consensus 142 ~~~~~A~~~I~~li~g~ 158 (180)
T PRK13763 142 EQVEIAREAIEMLIEGA 158 (180)
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 99999999999988665
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=99.31 E-value=4.3e-12 Score=101.79 Aligned_cols=65 Identities=28% Similarity=0.473 Sum_probs=58.8
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 435 (596)
+.+|.||.+.+|+|||++|++|++|++.|||+|++.+..+ ....+|.|+|+|++++++.|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~~~----~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVL----PGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCCCC----CCCCceEEEEEeCHHHHHHHHHhhC
Confidence 3689999999999999999999999999999999987554 2577899999999999999999983
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=99.31 E-value=3.4e-12 Score=102.36 Aligned_cols=65 Identities=31% Similarity=0.534 Sum_probs=59.5
Q ss_pred EEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHH
Q 007603 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVT 195 (596)
Q Consensus 130 t~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~ 195 (596)
++||+||...+|+||||+|++|++|+++|||+|.+.+. ..+...+|+|+|+|++++|.+|+.+|.
T Consensus 1 ~~r~~ip~~~vg~iIG~~G~~i~~i~~~tga~I~i~~~-~~~~~~~r~v~I~G~~~~v~~A~~~I~ 65 (65)
T cd02396 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS-VLPGSTERVVTISGKPSAVQKALLLIL 65 (65)
T ss_pred CEEEEECHHHcCeeECCCcHHHHHHHHHHCCEEEEcCC-CCCCCCceEEEEEeCHHHHHHHHHhhC
Confidence 37899999999999999999999999999999999984 334788999999999999999999873
No 17
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.26 E-value=3.8e-11 Score=128.17 Aligned_cols=269 Identities=20% Similarity=0.226 Sum_probs=173.3
Q ss_pred CCCCCCCCcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccC
Q 007603 16 GPLNLPDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEG 95 (596)
Q Consensus 16 ~~~~~~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~ 95 (596)
+..+..++++.+.+.|++..+..+|||.|++|+.|++.|++||.+.+...+ ++++.++.|-+..
T Consensus 59 ~~e~e~~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~ed~g-~e~~~~~~~~p~~--------------- 122 (608)
T KOG2279|consen 59 TEEQKPQKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTEDVG-DERVLLISGFPVQ--------------- 122 (608)
T ss_pred ceecCchhheeeeEeecccceeeeeccccCCcchhhcccccceecCcccCC-cccchhhccCCCC---------------
Confidence 345667889999999999999999999999999999999999999765433 5677777775543
Q ss_pred CCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCC
Q 007603 96 GEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDD 175 (596)
Q Consensus 96 ~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~d 175 (596)
+++|..++.. ++... ..+...+-+|...++.|+|++|.+++.|+..++|+|.+..+ .-...+
T Consensus 123 --v~~a~a~~~~---~~~~~-----------~pvk~~lsvpqr~~~~i~grgget~~si~~ss~aki~~d~n--gr~g~~ 184 (608)
T KOG2279|consen 123 --VCKAKAAIHQ---ILTEN-----------TPVSEQLSVPQRSVGRIIGRGGETIRSICKSSGAKITCDKN--GRLGLS 184 (608)
T ss_pred --CChHHHHHHH---HHhcC-----------Ccccccccchhhhcccccccchhhhcchhcccccccccccc--cccccc
Confidence 4555444332 22221 25677789999999999999999999999999999999874 334578
Q ss_pred cEEEEeecHHHHHHHHHHHHHHHhccCCCCC-------CCcccCCCccccccCCCCCCCCCcCCC------cCCCCCCCC
Q 007603 176 QLIQITGATLAVKKALVAVTTCLQHLSTMEK-------SPICFNRPIEKVFYSNSSDPHREFFPH------LSLVPPLTG 242 (596)
Q Consensus 176 RiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~-------~~~~~~~P~~~~~~~~~~~~~~~~~p~------~~~~p~~~~ 242 (596)
++..|.|...-+..|..++.+.+.+.-...+ ...+...|.... ......+.....++ .++.|..++
T Consensus 185 ~~~~i~~qqk~~~~a~~~~~~~~~edeelv~~~~e~~q~rvprk~p~n~~-~~~m~~~~~s~~~h~~~~t~~s~spg~~~ 263 (608)
T KOG2279|consen 185 RLIKISGQQKEVAAAKHLILEKVSEDEELVKRIAESAQTRVPRKQPINVR-REDMTEPGGAGEPHLWKNTSSSMSPGAPL 263 (608)
T ss_pred cceecccccchHHHHHhhhhccccchhHHhhhchhhcccCCCCCCCcccc-chhhcccccCCccccCccchhccCCCCCC
Confidence 8999999999999999999999876421111 001111111110 00000011111111 122222111
Q ss_pred CCCC---CC-----CcccCCCCCCCCCCCCCCccCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCC
Q 007603 243 NPSD---NA-----SEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLT 314 (596)
Q Consensus 243 ~~~~---ya-----~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~ 314 (596)
...+ .. .++|. ....+. .........++|.+|...+|.+||+.|+.++.+...+++.+.|.-...
T Consensus 264 ~~~eg~dm~v~vsk~~s~~--~~~d~s-----~~k~~~l~i~e~e~p~~lsg~lig~~gey~s~yssasn~~~hi~t~py 336 (608)
T KOG2279|consen 264 VTKEGGDMAVVVSKEGSWE--KPSDDS-----FQKSEALAIPEMEMPEILSGDLIGHAGEYLSVYSSASNHPNHIWTQPY 336 (608)
T ss_pred cccCCCcceeEEecccccC--Cccccc-----cccccccccceeecCcccccchhhhhhhhhhhhhhccCccceEEeccc
Confidence 1100 00 00000 000000 011223346778899999999999999999999999999999874322
Q ss_pred CC---CccEEEEEec
Q 007603 315 KS---GERVVTISAL 326 (596)
Q Consensus 315 ~~---~er~v~IsG~ 326 (596)
.+ .-.++.+.|+
T Consensus 337 t~~v~~~qic~~egk 351 (608)
T KOG2279|consen 337 TSRVLQLQICVNEGK 351 (608)
T ss_pred cchhhhhhhheecch
Confidence 22 1256777786
No 18
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=99.21 E-value=5.3e-11 Score=127.06 Aligned_cols=231 Identities=18% Similarity=0.212 Sum_probs=169.5
Q ss_pred CCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCC
Q 007603 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTME 205 (596)
Q Consensus 126 ~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~ 205 (596)
...+.+++.|+...+.+++||.|++|+.|+..++++|.+..+ .-..++...+.|-+.++.+|...++.++.+..
T Consensus 65 ~k~v~~e~Vv~~e~vkli~gr~gsnik~l~~~t~aKi~L~~e---d~g~e~~~~~~~~p~~v~~a~a~~~~~~~~~~--- 138 (608)
T KOG2279|consen 65 QKDIEIEMVVPQEAVKLIIGRQGSNIKQLRKQTGAKIDLDTE---DVGDERVLLISGFPVQVCKAKAAIHQILTENT--- 138 (608)
T ss_pred hhheeeeEeecccceeeeeccccCCcchhhcccccceecCcc---cCCcccchhhccCCCCCChHHHHHHHHHhcCC---
Confidence 346889999999999999999999999999999999999774 22345555666689999999999999997631
Q ss_pred CCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccCCCcceEEEEEeccccc
Q 007603 206 KSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTA 285 (596)
Q Consensus 206 ~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~v 285 (596)
.+...+.+|...+
T Consensus 139 -------------------------------------------------------------------pvk~~lsvpqr~~ 151 (608)
T KOG2279|consen 139 -------------------------------------------------------------------PVSEQLSVPQRSV 151 (608)
T ss_pred -------------------------------------------------------------------cccccccchhhhc
Confidence 2344466899999
Q ss_pred cccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhc---------------
Q 007603 286 SGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV--------------- 350 (596)
Q Consensus 286 g~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~--------------- 350 (596)
++|+|++|.+++.|+.-++|+|.+..+-...-.+...|.+.. ++...|-.++.+++.++
T Consensus 152 ~~i~grgget~~si~~ss~aki~~d~ngr~g~~~~~~i~~qq------k~~~~a~~~~~~~~~edeelv~~~~e~~q~rv 225 (608)
T KOG2279|consen 152 GRIIGRGGETIRSICKSSGAKITCDKNGRLGLSRLIKISGQQ------KEVAAAKHLILEKVSEDEELVKRIAESAQTRV 225 (608)
T ss_pred ccccccchhhhcchhcccccccccccccccccccceeccccc------chHHHHHhhhhccccchhHHhhhchhhcccCC
Confidence 999999999999999999999999976444456777777763 22223333333333221
Q ss_pred -------cc-----------------------cCCCCC-----------------------CC--CCCCceEEEEEeccc
Q 007603 351 -------EG-----------------------QQGFSS-----------------------GE--NKGDAVAVSILVGAD 375 (596)
Q Consensus 351 -------~~-----------------------~~g~~~-----------------------g~--~~~~~~t~~l~VP~~ 375 (596)
.+ ..|.+. +. ......-.+|.||..
T Consensus 226 prk~p~n~~~~~m~~~~~s~~~h~~~~t~~s~spg~~~~~~eg~dm~v~vsk~~s~~~~~d~s~~k~~~l~i~e~e~p~~ 305 (608)
T KOG2279|consen 226 PRKQPINVRREDMTEPGGAGEPHLWKNTSSSMSPGAPLVTKEGGDMAVVVSKEGSWEKPSDDSFQKSEALAIPEMEMPEI 305 (608)
T ss_pred CCCCCccccchhhcccccCCccccCccchhccCCCCCCcccCCCcceeEEecccccCCccccccccccccccceeecCcc
Confidence 00 001000 00 012345678999999
Q ss_pred cccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHH
Q 007603 376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGR 437 (596)
Q Consensus 376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~ 437 (596)
.+|.|||+.|+.++.....+++.+.|--....-. --.-.++.+.|+..-+..++.|+..+
T Consensus 306 lsg~lig~~gey~s~yssasn~~~hi~t~pyt~~--v~~~qic~~egkqh~~n~vl~ml~~~ 365 (608)
T KOG2279|consen 306 LSGDLIGHAGEYLSVYSSASNHPNHIWTQPYTSR--VLQLQICVNEGKQHYENSVLEMLTVH 365 (608)
T ss_pred cccchhhhhhhhhhhhhhccCccceEEeccccch--hhhhhhheecchhHHHHHHHhhhhcc
Confidence 9999999999999999999999999975322100 01126788999999999999998743
No 19
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.18 E-value=4.7e-11 Score=94.73 Aligned_cols=60 Identities=20% Similarity=0.325 Sum_probs=55.5
Q ss_pred EEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007603 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (596)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 434 (596)
.+|.||.+++++|||++|++|++|++.|||+|.|++.. ..++.|+|+|+.++|..|+.+|
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 57999999999999999999999999999999998743 4689999999999999999987
No 20
>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=99.13 E-value=4.2e-11 Score=94.36 Aligned_cols=60 Identities=27% Similarity=0.422 Sum_probs=54.9
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 434 (596)
|.+|.||.+++|+|||++|++|++|++.|||+|+|++. + ++..|+|+|++++|+.|+.+|
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 67999999999999999999999999999999999763 2 356999999999999999986
No 21
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.11 E-value=1.8e-10 Score=91.12 Aligned_cols=58 Identities=16% Similarity=0.271 Sum_probs=53.6
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCC-HHHHHHHHHHH
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGE-YKNVQNALSEV 434 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~-~~~V~~A~~~I 434 (596)
.+..+.||.+++|+|||++|++|++|+++|||+|.|++ ++.|.|+|+ +++++.|+.+|
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 46789999999999999999999999999999999964 467999999 99999999987
No 22
>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=99.05 E-value=4.7e-10 Score=89.13 Aligned_cols=62 Identities=26% Similarity=0.489 Sum_probs=56.6
Q ss_pred EEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHH
Q 007603 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEV 434 (596)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I 434 (596)
.++.||.+++++|||++|++|++|++.|||+|.|+.... ...++.|+|+|+.+++..|+.+|
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 589999999999999999999999999999999987443 35689999999999999999887
No 23
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=99.03 E-value=1.8e-09 Score=124.53 Aligned_cols=320 Identities=18% Similarity=0.200 Sum_probs=198.3
Q ss_pred cEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCC-----ceEEEEccCcchhhhhhhc-ccccc-----
Q 007603 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSD-----HRVILVVGSGSIDRRIMFC-ENDVV----- 92 (596)
Q Consensus 24 ~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~-----eRvi~I~G~~e~~~~a~~~-~~~~~----- 92 (596)
-+..++.+....+..+||++|.+++.++.++.+.|+|++.....+ .+..-+....-+...+... +.+..
T Consensus 200 ~~~~k~~v~~~~~~~~~g~g~~~~~~~~d~~~~~i~ip~sn~~~~~~~i~~~~~~~~~~~~~i~~~~~~le~~~~~~~~~ 279 (753)
T KOG2208|consen 200 SVFEKMNVGITLHSHIIGRGGSNISIIMDETKVHIHIPDSNKSSPSNKIDGRLNSSSSINVEIQEALTRLESEFDYDEII 279 (753)
T ss_pred eEEEEeeccccchhhhccccccccccccccceeEEEcccccccchhhhhccccccceehhhhhHHHHHHhcChhhhhhhh
Confidence 477889999999999999999999999999999999976422211 1111111111111111111 00000
Q ss_pred ------ccCCCccHHHHHHHHHHHHHHhhhhc----cC------CC---------------CCCCCceEEEEEeccceee
Q 007603 93 ------VEGGEVSSTQEAVIRVFERMWEVEAE----VE------GD---------------GDGDDVAYCGLLANTTKIG 141 (596)
Q Consensus 93 ------~e~~~~~~A~~Al~~i~~~i~~~~~~----~~------~~---------------~~~~~~vt~rllVp~~~vG 141 (596)
..........+.+...+..+...... .+ .+ ......+.+.+-+....+.
T Consensus 280 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nn~~i~~~i~~~~~~ 359 (753)
T KOG2208|consen 280 YRRLPRFIRGIPGEEINQLRDYMPEVDSIFQNYPSKDDSIVLSGFEVGAVLAKRDKTLLLKNSEENNENIKREIFPEELK 359 (753)
T ss_pred hccccccccccccchhhHHHhhcchhhhhhccccccceeEeecccccchhhhhhHHHHHHHHhhccceeeEEeecHHhhh
Confidence 00000011111111111111100000 00 00 0011236677888899999
Q ss_pred eeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccC
Q 007603 142 VVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYS 221 (596)
Q Consensus 142 ~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~ 221 (596)
.++||+|.+|.+|++++.+.|.+.. .++.+..+.++|...++.+|...|.....+....
T Consensus 360 ~v~GK~~~ni~ki~e~~~~~i~~~~----~~~~~~~v~~~~~~~~~~ka~~~v~~~~~ei~n~----------------- 418 (753)
T KOG2208|consen 360 FVIGKKGANIEKIREESQVKIDLPK----QGSNNKKVVITGVSANDEKAVEDVEKIIAEILNS----------------- 418 (753)
T ss_pred hhcCCCCccHHHHHHhhhhceeccc----ccCCCCCeEEeccccchhHHHHHHHHHHHhhhcc-----------------
Confidence 9999999999999999999999966 4678899999999999999999999999873210
Q ss_pred CCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCCCCCccCCCcceEEEEEeccccccccccccchhhhhhhh
Q 007603 222 NSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHPGLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQN 301 (596)
Q Consensus 222 ~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~ 301 (596)
.....+.+|...+..+||.+|..|..|..
T Consensus 419 ---------------------------------------------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~ 447 (753)
T KOG2208|consen 419 ---------------------------------------------------IVKEEVQIPTKSHKRIIGTKGALINYIMG 447 (753)
T ss_pred ---------------------------------------------------cccceeecCccchhhhhccccccHHHHHh
Confidence 12334679999999999999999999999
Q ss_pred ccC-eeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEecccccccc
Q 007603 302 ASG-ALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCL 380 (596)
Q Consensus 302 ~tG-a~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~I 380 (596)
+++ ..|++... ......+++.|.. ..+.. +..++........ ....-...+.+.+.|..+.+..
T Consensus 448 k~~~v~i~f~~~--~~~~~~~~~~~~~---~dv~~---~~~~~~~~~~~a~-------~~~~~~~~~~d~~~~~~~~~~~ 512 (753)
T KOG2208|consen 448 KHGGVHIKFQNN--NNSSDMVTIRGIS---KDVEK---SVSLLKALKADAK-------NLKFRDVVTKDKLLPVKYIGKE 512 (753)
T ss_pred hcCcEEEecCCC--CcccccceEeccc---cccch---hHHHHHhhhhhhh-------cchhhhhhhccccchHHhhccc
Confidence 999 55555443 3334456777753 11111 1211111110000 0001234566777777777777
Q ss_pred ccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007603 381 TGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 381 IGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (596)
+|+.|..+...++.....+.. ..++..++|.|..+.|.+|..++...+..
T Consensus 513 ~g~~~~i~d~~~~~~i~~~~~----------~~~~~~i~i~gk~~~v~~a~~~L~~~~~~ 562 (753)
T KOG2208|consen 513 IGKNGTIRDSLGDKSIFPPNE----------DEDHEKITIEGKLELVLEAPAELKALIEA 562 (753)
T ss_pred ccCceeeeccCCceeeccccc----------ccccceeeecccccchhhhHHHHHhcchh
Confidence 777777666555444444432 25688999999999999999999876653
No 24
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.01 E-value=3.7e-10 Score=89.56 Aligned_cols=60 Identities=27% Similarity=0.354 Sum_probs=55.3
Q ss_pred EEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007603 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (596)
Q Consensus 131 ~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I 194 (596)
.+|.||..++++|||++|++|++|+++|||+|.+... ...++.|+|+|+.++|.+|+.+|
T Consensus 2 ~~i~Vp~~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~----~~~~~~v~I~G~~~~v~~A~~~i 61 (62)
T cd02394 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDP----GSKSDTITITGPKENVEKAKEEI 61 (62)
T ss_pred eEEEeCHHHhhhccCCCCCcHHHHHHHhCCEEEcCCC----CCCCCEEEEEcCHHHHHHHHHHh
Confidence 5689999999999999999999999999999999873 26789999999999999999886
No 25
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=99.01 E-value=1.6e-10 Score=90.97 Aligned_cols=60 Identities=23% Similarity=0.418 Sum_probs=54.8
Q ss_pred EEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007603 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (596)
Q Consensus 130 t~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I 194 (596)
|.+|.||..++++|||++|++|++|+++|||+|.|.++ + ....|+|+|+.++|.+|+.+|
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 67899999999999999999999999999999999772 2 455999999999999999886
No 26
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.94 E-value=1.8e-09 Score=85.81 Aligned_cols=62 Identities=31% Similarity=0.532 Sum_probs=56.3
Q ss_pred EEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHH
Q 007603 131 CGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAV 194 (596)
Q Consensus 131 ~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I 194 (596)
.++.||..++++|||++|++|++|+++|||+|.|... .....++.|.|.|..+++.+|+.+|
T Consensus 2 ~~i~ip~~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~--~~~~~~~~v~i~G~~~~v~~a~~~i 63 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDS--GSGSEERIVTITGTPEAVEKAKELI 63 (64)
T ss_pred EEEEEchhhcceeECCCCHHHHHHHHHHCCEEEEcCC--CCCCCceEEEEEcCHHHHHHHHHHh
Confidence 5799999999999999999999999999999999873 2246789999999999999999886
No 27
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.93 E-value=2.2e-09 Score=84.91 Aligned_cols=58 Identities=26% Similarity=0.343 Sum_probs=52.8
Q ss_pred eEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHH
Q 007603 129 AYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAV 194 (596)
Q Consensus 129 vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~-~e~V~~A~~~I 194 (596)
.+..+-||...+|+||||+|++|++|+++|||+|.|.. ++.|.|+|. .+++.+|+.+|
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 45678899999999999999999999999999999965 367999998 99999999887
No 28
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=98.83 E-value=5.6e-09 Score=120.47 Aligned_cols=286 Identities=16% Similarity=0.167 Sum_probs=189.3
Q ss_pred EEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHH
Q 007603 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEA 104 (596)
Q Consensus 25 ~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~A 104 (596)
....+-+-......|+||+|.+|.+|+++++|.|.+... +..+..+.+++..++ +..|.+.
T Consensus 347 ~~i~~~i~~~~~~~v~GK~~~ni~ki~e~~~~~i~~~~~--~~~~~~v~~~~~~~~-----------------~~ka~~~ 407 (753)
T KOG2208|consen 347 ENIKREIFPEELKFVIGKKGANIEKIREESQVKIDLPKQ--GSNNKKVVITGVSAN-----------------DEKAVED 407 (753)
T ss_pred eeeEEeecHHhhhhhcCCCCccHHHHHHhhhhceecccc--cCCCCCeEEeccccc-----------------hhHHHHH
Confidence 445556677889999999999999999999999999873 456678889987766 4446566
Q ss_pred HHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccc-cEEEecCCCCCCCCCCcEEEEeec
Q 007603 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESG-AKIVMLPPPACAAIDDQLIQITGA 183 (596)
Q Consensus 105 l~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esG-a~I~I~~~p~~~~~~dRiV~I~G~ 183 (596)
+..++..+... .+...+.+|...+..|||.+|..|..|.+++| ..|+... .......+++.|.
T Consensus 408 v~~~~~ei~n~------------~~~~~~~iP~k~~~~iig~~g~~i~~I~~k~~~v~i~f~~----~~~~~~~~~~~~~ 471 (753)
T KOG2208|consen 408 VEKIIAEILNS------------IVKEEVQIPTKSHKRIIGTKGALINYIMGKHGGVHIKFQN----NNNSSDMVTIRGI 471 (753)
T ss_pred HHHHHHhhhcc------------cccceeecCccchhhhhccccccHHHHHhhcCcEEEecCC----CCcccccceEecc
Confidence 66655554331 34455899999999999999999999999999 6666654 3445556788888
Q ss_pred HHHHHHHHHHHHHHHhccCCCCCCCcccCCCccccccCCCCCCCCCcCCCcCCCCCCCCCCCCCCCcccCCCCCCCCCCC
Q 007603 184 TLAVKKALVAVTTCLQHLSTMEKSPICFNRPIEKVFYSNSSDPHREFFPHLSLVPPLTGNPSDNASEFHSSSADADRDHP 263 (596)
Q Consensus 184 ~e~V~~A~~~I~~~L~e~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~p~~~~~p~~~~~~~~ya~~~~p~~~~~~r~~p 263 (596)
...|.++..+...+........
T Consensus 472 ~~dv~~~~~~~~~~~~~a~~~~---------------------------------------------------------- 493 (753)
T KOG2208|consen 472 SKDVEKSVSLLKALKADAKNLK---------------------------------------------------------- 493 (753)
T ss_pred ccccchhHHHHHhhhhhhhcch----------------------------------------------------------
Confidence 8888877766665554321100
Q ss_pred CCCccCCCcceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHH
Q 007603 264 GLDKKGRKQEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLV 343 (596)
Q Consensus 264 ~~~~~~~~~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i 343 (596)
.....+.....|..+.+..+|+.|..+....++....+..+ ..+..++|.|.. ..+.+|...+
T Consensus 494 ------~~~~~~~d~~~~~~~~~~~~g~~~~i~d~~~~~~i~~~~~~-----~~~~~i~i~gk~------~~v~~a~~~L 556 (753)
T KOG2208|consen 494 ------FRDVVTKDKLLPVKYIGKEIGKNGTIRDSLGDKSIFPPNED-----EDHEKITIEGKL------ELVLEAPAEL 556 (753)
T ss_pred ------hhhhhhccccchHHhhcccccCceeeeccCCceeecccccc-----cccceeeecccc------cchhhhHHHH
Confidence 00111233456677777777777766666655554433222 345678888875 2222333333
Q ss_pred HhhhhhccccCCCCCCCCCCCceEEEEEecc-ccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcC
Q 007603 344 FARSVEVEGQQGFSSGENKGDAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422 (596)
Q Consensus 344 ~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G 422 (596)
...+... .......+.+|. ...-++++++....+..+...|+.+.+++. ....+.++|.|
T Consensus 557 ~~~~~~~------------~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~e~~~gv~~~fp~~-------~~~~~e~~i~g 617 (753)
T KOG2208|consen 557 KALIEAL------------IKATLLEVNNPPGQHRPFLIGKGIENRTYVEVFGGVVVPFPRS-------PTSSDEVSIKG 617 (753)
T ss_pred Hhcchhh------------hhhhhhhccCcchheeeeeeccccccccceeecCcccccCCCC-------CCchhhhccch
Confidence 3332110 011233444444 455566666666666666666788888763 34556899999
Q ss_pred CHHHHHHHHHHHHHHHh
Q 007603 423 EYKNVQNALSEVVGRLR 439 (596)
Q Consensus 423 ~~~~V~~A~~~I~~~Lr 439 (596)
....++.|...+.....
T Consensus 618 ~~~~v~aa~~~~~~i~~ 634 (753)
T KOG2208|consen 618 AKDEVKAAKGRLEEIVE 634 (753)
T ss_pred hHHHHHHhhccchhhhh
Confidence 99999999998877655
No 29
>PF13014 KH_3: KH domain
Probab=98.80 E-value=8.8e-09 Score=75.53 Aligned_cols=42 Identities=40% Similarity=0.727 Sum_probs=38.5
Q ss_pred ccceeecCCChHHHHHHHHhCceEEEeC-CCCCCCceEEEEcc
Q 007603 35 VVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVG 76 (596)
Q Consensus 35 ~vg~IIGk~G~~Ik~Ir~eTga~I~V~~-~~~g~~eRvi~I~G 76 (596)
++|+|||++|++|++|+++|||+|+|++ ..++..+|+|+|+|
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 5799999999999999999999999988 56678899999987
No 30
>smart00322 KH K homology RNA-binding domain.
Probab=98.77 E-value=3.6e-08 Score=78.36 Aligned_cols=66 Identities=30% Similarity=0.534 Sum_probs=59.6
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL 438 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~L 438 (596)
.+.++.||.++++++||++|++|++|++.||++|.+.... .....|+|.|+.++++.|..+|...+
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 5789999999999999999999999999999999997522 25789999999999999999998876
No 31
>PF13014 KH_3: KH domain
Probab=98.76 E-value=9.9e-09 Score=75.26 Aligned_cols=43 Identities=35% Similarity=0.664 Sum_probs=37.9
Q ss_pred cccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcC
Q 007603 376 FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG 422 (596)
Q Consensus 376 ~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G 422 (596)
+||+|||++|++|++|+++|||+|+|++ +.. ....++.|+|+|
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~-~~~---~~~~~~~v~I~G 43 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP-ENE---PGSNERVVTITG 43 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC-ccC---CCCCceEEEEEC
Confidence 5899999999999999999999999998 221 367899999998
No 32
>smart00322 KH K homology RNA-binding domain.
Probab=98.63 E-value=1.2e-07 Score=75.39 Aligned_cols=67 Identities=27% Similarity=0.487 Sum_probs=60.4
Q ss_pred ceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHH
Q 007603 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCL 198 (596)
Q Consensus 128 ~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L 198 (596)
.++.++.||...++.+||++|++|++|++.||++|.+... .....++.|.|..+++..|..+|.+.+
T Consensus 2 ~~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~----~~~~~~v~i~g~~~~v~~a~~~i~~~~ 68 (69)
T smart00322 2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPED----GSEERVVEITGPPENVEKAAELILEIL 68 (69)
T ss_pred ceEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCC----CCCccEEEEEcCHHHHHHHHHHHHHHh
Confidence 4678899999999999999999999999999999999763 226789999999999999999998876
No 33
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.52 E-value=1.8e-07 Score=89.46 Aligned_cols=141 Identities=17% Similarity=0.211 Sum_probs=98.4
Q ss_pred CcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCc---chhh--hhh---hcccccccc
Q 007603 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSG---SIDR--RIM---FCENDVVVE 94 (596)
Q Consensus 23 ~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~---e~~~--~a~---~~~~~~~~e 94 (596)
....+.+.+|.+..+.+||+.|++.+.|.+.++++|.++ ..+..|.|..+. ++.. +|. ..++..
T Consensus 6 ~~~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD-----~~~~~V~i~~~~~t~Dp~~~~ka~d~VkAIgrG--- 77 (194)
T COG1094 6 EKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRID-----SKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG--- 77 (194)
T ss_pred ccceeeeecCchhheeeecccccchHHHHhhcCeEEEEE-----CCCCeEEEEecCCCCChHHHHHHHHHHHHHhcC---
Confidence 445677999999999999999999999999999999995 345778887552 2211 000 001111
Q ss_pred CCCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEE-----Eec------cceeeeeeecCchhhhhhccccccEEE
Q 007603 95 GGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGL-----LAN------TTKIGVVVGKGGRNVTRMRIESGAKIV 163 (596)
Q Consensus 95 ~~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rl-----lVp------~~~vG~IIGKgG~~Ik~I~~esGa~I~ 163 (596)
+++ ..|+.. ++. .+.+.+ ++. ....|+|||++|.+-+.|++-|||+|.
T Consensus 78 ---F~p-e~A~~L-L~d----------------~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~ 136 (194)
T COG1094 78 ---FPP-EKALKL-LED----------------DYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYIS 136 (194)
T ss_pred ---CCH-HHHHHH-hcC----------------CcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEE
Confidence 111 111111 110 111111 111 134699999999999999999999999
Q ss_pred ecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcc
Q 007603 164 MLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 164 I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~ 201 (596)
|.. ..|.|-|.+++|+.|..+|..++...
T Consensus 137 V~g---------~tVaiiG~~~~v~iAr~AVemli~G~ 165 (194)
T COG1094 137 VYG---------KTVAIIGGFEQVEIAREAVEMLINGA 165 (194)
T ss_pred EeC---------cEEEEecChhhhHHHHHHHHHHHcCC
Confidence 954 67999999999999999999999874
No 34
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=98.47 E-value=8.4e-07 Score=84.88 Aligned_cols=143 Identities=18% Similarity=0.217 Sum_probs=98.2
Q ss_pred eEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhcccc
Q 007603 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQ 353 (596)
Q Consensus 274 ~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~ 353 (596)
....+.||...++.+||+.|...+.|.+.++++|.++. .+..|+|..++...++. ....|.- .+ ..+.
T Consensus 8 ~~~~v~iPk~R~~~lig~~g~v~k~ie~~~~~~~~iD~-----~~~~V~i~~~~~t~Dp~-~~~ka~d----~V--kAIg 75 (194)
T COG1094 8 SSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDS-----KTGSVTIRTTRKTEDPL-ALLKARD----VV--KAIG 75 (194)
T ss_pred ceeeeecCchhheeeecccccchHHHHhhcCeEEEEEC-----CCCeEEEEecCCCCChH-HHHHHHH----HH--HHHh
Confidence 35668899999999999999999999999999999983 34568887763111111 1122211 11 1123
Q ss_pred CCCCCCC----CCCCceEEEEE----e--c----cccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEE
Q 007603 354 QGFSSGE----NKGDAVAVSIL----V--G----ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQ 419 (596)
Q Consensus 354 ~g~~~g~----~~~~~~t~~l~----V--P----~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~ 419 (596)
.|+++.- -.....-..+. + + ....|+|||++|.+.+-|++.|||.|-|.. ..|.
T Consensus 76 rGF~pe~A~~LL~d~~~levIdi~~~~~~~~~~l~R~kgRIIG~~GkTr~~IE~lt~~~I~V~g------------~tVa 143 (194)
T COG1094 76 RGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKTRRAIEELTGVYISVYG------------KTVA 143 (194)
T ss_pred cCCCHHHHHHHhcCCcEEEEEEHHHhccCchhhhhHhhceeeCCCchHHHHHHHHhCCeEEEeC------------cEEE
Confidence 3333210 00011111111 0 1 236799999999999999999999999963 6799
Q ss_pred EcCCHHHHHHHHHHHHHHHhh
Q 007603 420 ISGEYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 420 I~G~~~~V~~A~~~I~~~Lr~ 440 (596)
|-|.+++|+.|.+.|...+..
T Consensus 144 iiG~~~~v~iAr~AVemli~G 164 (194)
T COG1094 144 IIGGFEQVEIAREAVEMLING 164 (194)
T ss_pred EecChhhhHHHHHHHHHHHcC
Confidence 999999999999999988764
No 35
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.11 E-value=7e-06 Score=73.86 Aligned_cols=67 Identities=19% Similarity=0.362 Sum_probs=53.2
Q ss_pred ccccccccCCCchhHHHHHHhCCeEEEeCCCcc-----------ccc-CCCCCcEEEEcCCH---HHHHHHHHHHHHHHh
Q 007603 375 DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV-----------LGC-AAQNDVVIQISGEY---KNVQNALSEVVGRLR 439 (596)
Q Consensus 375 ~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~-----------P~~-~~~~er~V~I~G~~---~~V~~A~~~I~~~Lr 439 (596)
+++|.|||++|++||+|+++|||+|.|..+... |.+ ...+.-.|.|++.. +++++|..+|...|.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 689999999999999999999999999875211 111 12334789999975 899999999998887
Q ss_pred hc
Q 007603 440 HN 441 (596)
Q Consensus 440 ~~ 441 (596)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 43
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=98.00 E-value=1.3e-05 Score=72.04 Aligned_cols=64 Identities=23% Similarity=0.337 Sum_probs=51.8
Q ss_pred ceeeeeeecCchhhhhhccccccEEEecCCCC---------------CCCCCCcEEEEeec---HHHHHHHHHHHHHHHh
Q 007603 138 TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPA---------------CAAIDDQLIQITGA---TLAVKKALVAVTTCLQ 199 (596)
Q Consensus 138 ~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~---------------~~~~~dRiV~I~G~---~e~V~~A~~~I~~~L~ 199 (596)
+.+|.|||++|++||+|+++|||+|.|..+.. .....+-.|.|++. .+++.+|+.+|..++.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~~~~~~~~eplhV~I~a~~~~~e~~~~A~~~I~~ll~ 94 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPKYAHLNEPLHVLITAETPPEEALAKAVEAIEELLK 94 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccCcccccCCCCcEEEEEeCCcHHHHHHHHHHHHHHHhc
Confidence 67899999999999999999999999987400 00123357889996 4999999999999998
Q ss_pred cc
Q 007603 200 HL 201 (596)
Q Consensus 200 e~ 201 (596)
..
T Consensus 95 ~~ 96 (120)
T cd02395 95 PA 96 (120)
T ss_pred cC
Confidence 53
No 37
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.80 E-value=4e-05 Score=70.90 Aligned_cols=103 Identities=14% Similarity=0.146 Sum_probs=68.6
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHH
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAV 105 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al 105 (596)
.+.++|+...+|+.||++|++|+.|++..|-+|+|=....+ .+ +-+
T Consensus 33 ~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d-----------~~-----------------------~fI 78 (140)
T PRK08406 33 RIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD-----------PE-----------------------EFI 78 (140)
T ss_pred EEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC-----------HH-----------------------HHH
Confidence 45678899999999999999999999999988887432111 10 111
Q ss_pred HHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEec
Q 007603 106 IRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (596)
Q Consensus 106 ~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~ 165 (596)
..++....-....- ...+....+.+.|+....|..|||+|++|+.++.-+|-++.|.
T Consensus 79 ~n~l~Pa~V~~v~I---~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 79 KNIFAPAAVRSVTI---KKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred HHHcCCCEEEEEEE---EecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 11111100000000 0011235667789999999999999999999999998877663
No 38
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.67 E-value=0.00016 Score=82.53 Aligned_cols=93 Identities=13% Similarity=0.195 Sum_probs=71.4
Q ss_pred chHHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCC
Q 007603 334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ 413 (596)
Q Consensus 334 ~~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~ 413 (596)
..+.++...|++.+.+..... .......+...++.||.+++|.|||+||++||+|+++|||+|.|.+
T Consensus 549 ~~A~~g~~~Il~~m~~al~~p---~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d---------- 615 (719)
T TIGR02696 549 KQARDARLAILDVMAEAIDTP---DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED---------- 615 (719)
T ss_pred HHHHHHHHHHHHHHHHHHhCc---cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec----------
Confidence 344566666776665432211 1122345678999999999999999999999999999999999964
Q ss_pred CCcEEEEcCC-HHHHHHHHHHHHHHHhh
Q 007603 414 NDVVIQISGE-YKNVQNALSEVVGRLRH 440 (596)
Q Consensus 414 ~er~V~I~G~-~~~V~~A~~~I~~~Lr~ 440 (596)
+..|.|.+. .+.+++|+.+|...++.
T Consensus 616 -~G~V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 616 -DGTVYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred -CcEEEEEeCCHHHHHHHHHHHHHhhCc
Confidence 577888885 77999999999987775
No 39
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.59 E-value=6.8e-05 Score=75.84 Aligned_cols=148 Identities=18% Similarity=0.260 Sum_probs=103.8
Q ss_pred cceEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHh---hhh
Q 007603 272 QEVALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA---RSV 348 (596)
Q Consensus 272 ~~~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~---~i~ 348 (596)
..++..+.+|..+++.+.|++|++||.++.+|...|+-+.. ..+-++.++|.. ..+..|-..|.. .+.
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr---~eePiF~vTg~~------edv~~aRrei~saaeH~~ 94 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR---GEEPIFPVTGRH------EDVRRARREIPSAAEHFG 94 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC---CCCCcceeccCc------hhHHHHhhcCccccceee
Confidence 56677888999999999999999999999999998876632 123578888863 112222221111 110
Q ss_pred hccccCCCC---CCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHH
Q 007603 349 EVEGQQGFS---SGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425 (596)
Q Consensus 349 e~~~~~g~~---~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~ 425 (596)
-....+.+. .+...+.+.+..+.+|-+.+|.|.|..|.+|+.||+.+...|.-+-+ ..+-+.-++|.+.
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 LIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPVR--------CGEPVFCVTGAPK 166 (394)
T ss_pred eeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeecc--------CCCceEEEecCCc
Confidence 000001111 12223567889999999999999999999999999999999987653 3477888999998
Q ss_pred H-HHHHH-HHHHH
Q 007603 426 N-VQNAL-SEVVG 436 (596)
Q Consensus 426 ~-V~~A~-~~I~~ 436 (596)
+ +++|. ..|+.
T Consensus 167 nC~kra~s~eie~ 179 (394)
T KOG2113|consen 167 NCVKRARSCEIEQ 179 (394)
T ss_pred chhhhccccchhh
Confidence 8 66666 45544
No 40
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=97.57 E-value=0.00014 Score=73.70 Aligned_cols=155 Identities=19% Similarity=0.209 Sum_probs=109.6
Q ss_pred CcEEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHH
Q 007603 23 DVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQ 102 (596)
Q Consensus 23 ~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~ 102 (596)
+.++..+-||...++.|.|++|-+||.||.+|.+.|+-+-. + .|-+..++|..+.+++|..++... |
T Consensus 24 ~nvt~sv~vps~~v~~ivg~qg~kikalr~KTqtyi~tPsr--~-eePiF~vTg~~edv~~aRrei~sa---------a- 90 (394)
T KOG2113|consen 24 QNVTESVEVPSEHVAEIVGRQGCKIKALRAKTQTYIKTPSR--G-EEPIFPVTGRHEDVRRARREIPSA---------A- 90 (394)
T ss_pred CccceeeecCcccceeecccCccccchhhhhhcceeccCCC--C-CCCcceeccCchhHHHHhhcCccc---------c-
Confidence 78899999999999999999999999999999999976432 1 345788899999988876654321 1
Q ss_pred HHHHHHHHHHHhhhhccCC-CCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEe
Q 007603 103 EAVIRVFERMWEVEAEVEG-DGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQIT 181 (596)
Q Consensus 103 ~Al~~i~~~i~~~~~~~~~-~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~ 181 (596)
.++-..+.......+. ........+...-+|-..+|.|.|..|.+|+.|++.++..|.-.- .| .+.+..++
T Consensus 91 ---eH~~l~~~s~s~Sgg~~~~s~s~qt~sy~svP~rvvglvv~~~~~ti~~iqq~tnt~I~T~v--~~---~~~Vf~Vt 162 (394)
T KOG2113|consen 91 ---EHFGLIRASRSFSGGTNGASASGQTTSYVSVPLRVVGLVVGPKGATIKRIQQFTNTYIATPV--RC---GEPVFCVT 162 (394)
T ss_pred ---ceeeeeeecccccCCCccccccCCCceeeeccceeeeeccccccCccchheecccceEeeec--cC---CCceEEEe
Confidence 0000000000000010 011234566777889999999999999999999999999988765 23 67788999
Q ss_pred ecHHH-HHHHH-HHHHHHH
Q 007603 182 GATLA-VKKAL-VAVTTCL 198 (596)
Q Consensus 182 G~~e~-V~~A~-~~I~~~L 198 (596)
|.+.+ +++|. ..|...+
T Consensus 163 g~~~nC~kra~s~eie~ta 181 (394)
T KOG2113|consen 163 GAPKNCVKRARSCEIEQTA 181 (394)
T ss_pred cCCcchhhhccccchhhhh
Confidence 99888 55555 4444433
No 41
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=97.54 E-value=0.00026 Score=65.53 Aligned_cols=102 Identities=16% Similarity=0.163 Sum_probs=71.5
Q ss_pred eEEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhh--hhcc
Q 007603 274 VALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARS--VEVE 351 (596)
Q Consensus 274 ~~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i--~e~~ 351 (596)
..+.++|+...+|..||++|++|+.|++..|-+|.+-.-..+ +.+-+..++..+ .+..
T Consensus 32 ~~vi~vV~~~~vG~~IG~~G~rI~~i~e~lgekIdVve~s~d--------------------~~~fI~n~l~Pa~V~~v~ 91 (140)
T PRK08406 32 DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDD--------------------PEEFIKNIFAPAAVRSVT 91 (140)
T ss_pred CEEEEEEeCCCccccCCcCchHHHHHHHHhCCceEEEEcCCC--------------------HHHHHHHHcCCCEEEEEE
Confidence 356688899999999999999999999999888877642111 111122221111 0000
Q ss_pred ccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEe
Q 007603 352 GQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (596)
Q Consensus 352 ~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~ 402 (596)
+. .........+.|+.+..|..|||+|++|+.++..+|-++.|.
T Consensus 92 I~-------~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di~ 135 (140)
T PRK08406 92 IK-------KKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDID 135 (140)
T ss_pred EE-------ecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCCe
Confidence 00 012235678889999999999999999999999999999774
No 42
>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=97.52 E-value=0.0003 Score=80.45 Aligned_cols=94 Identities=18% Similarity=0.232 Sum_probs=72.9
Q ss_pred ccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcE
Q 007603 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (596)
Q Consensus 98 ~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRi 177 (596)
+..|.++..+|+..+.+..... .+-....+....+-||.+.++.|||+||++||+|.++|||+|.|.. +..
T Consensus 548 L~~A~~g~~~Il~~m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--------~G~ 618 (719)
T TIGR02696 548 LKQARDARLAILDVMAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--------DGT 618 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--------CcE
Confidence 3456666667766655543333 2222333567778899999999999999999999999999999965 577
Q ss_pred EEEeec-HHHHHHHHHHHHHHHhc
Q 007603 178 IQITGA-TLAVKKALVAVTTCLQH 200 (596)
Q Consensus 178 V~I~G~-~e~V~~A~~~I~~~L~e 200 (596)
|.|.+. .+++.+|+.+|..++..
T Consensus 619 V~I~a~d~~~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 619 VYIGAADGPSAEAARAMINAIANP 642 (719)
T ss_pred EEEEeCCHHHHHHHHHHHHHhhCc
Confidence 888885 99999999999999974
No 43
>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=97.32 E-value=0.00042 Score=64.05 Aligned_cols=102 Identities=14% Similarity=0.141 Sum_probs=67.9
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcch-hhhhhhccccccccCCCccHHHHH
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSI-DRRIMFCENDVVVEGGEVSSTQEA 104 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~-~~~a~~~~~~~~~e~~~~~~A~~A 104 (596)
-+-++|....+|..||++|++|+.|++..|-+|+|=+...+ .+. ++++ ++||.
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D-----------~~~fI~N~-------------l~PA~-- 87 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSEN-----------LEEFVANK-------------LAPAE-- 87 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCC-----------HHHHHHHc-------------CCCce--
Confidence 45567888899999999999999999888988887432111 111 0000 11110
Q ss_pred HHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEec
Q 007603 105 VIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVML 165 (596)
Q Consensus 105 l~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~ 165 (596)
+..... ...++...+.+.|+..+.+..|||+|++|+..++-++-++.|.
T Consensus 88 -------V~~V~i-----~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 88 -------VKNVTV-----SEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred -------EEEEEE-----EcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 000000 0011245677889999999999999999999999988877664
No 44
>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=97.13 E-value=0.0011 Score=76.58 Aligned_cols=91 Identities=14% Similarity=0.225 Sum_probs=65.4
Q ss_pred HHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCC
Q 007603 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415 (596)
Q Consensus 336 a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~e 415 (596)
+.++...|++.+.+....... ..........++.||.+.+|.|||+||++||+|+++|||+|.|.+ +
T Consensus 523 a~~~~~~I~~~m~~~l~~~~~--~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d-----------d 589 (684)
T TIGR03591 523 AKEGRLHILGEMNKVISEPRA--ELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED-----------D 589 (684)
T ss_pred HHHHHHHHHHHHHHHHhhhhc--cccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec-----------C
Confidence 344555565555433211111 012235678899999999999999999999999999999999964 4
Q ss_pred cEEEEcC-CHHHHHHHHHHHHHHHh
Q 007603 416 VVIQISG-EYKNVQNALSEVVGRLR 439 (596)
Q Consensus 416 r~V~I~G-~~~~V~~A~~~I~~~Lr 439 (596)
..|.|.+ ..+.+++|..+|.....
T Consensus 590 G~V~i~~~~~~~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 590 GTVKIAASDGEAAEAAIKMIEGITA 614 (684)
T ss_pred eEEEEEECcHHHHHHHHHHHHhhhc
Confidence 5577766 46789999999987654
No 45
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.06 E-value=0.0011 Score=76.68 Aligned_cols=94 Identities=21% Similarity=0.262 Sum_probs=68.8
Q ss_pred cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEE
Q 007603 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (596)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV 178 (596)
..|.++..+|+..+.+...+.........+....+-||...++.|||++|++||+|+++|||+|.|.. +..|
T Consensus 521 ~~a~~~~~~I~~~m~~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~d--------dG~V 592 (684)
T TIGR03591 521 EQAKEGRLHILGEMNKVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIED--------DGTV 592 (684)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEec--------CeEE
Confidence 34555555666555444333222222333567778899999999999999999999999999999965 4567
Q ss_pred EEee-cHHHHHHHHHHHHHHHhc
Q 007603 179 QITG-ATLAVKKALVAVTTCLQH 200 (596)
Q Consensus 179 ~I~G-~~e~V~~A~~~I~~~L~e 200 (596)
.|.+ ..+.+.+|..+|..+..+
T Consensus 593 ~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 593 KIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred EEEECcHHHHHHHHHHHHhhhcc
Confidence 7776 589999999999988653
No 46
>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=97.01 E-value=0.0026 Score=58.88 Aligned_cols=101 Identities=14% Similarity=0.124 Sum_probs=69.8
Q ss_pred EEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHH--hhhhhccc
Q 007603 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEG 352 (596)
Q Consensus 275 ~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~--~~i~e~~~ 352 (596)
.+-++|....+|..||++|.+|+.|++..|-+|.+-.-..+.. +-+..++ .++.....
T Consensus 34 riifvV~~g~vG~~IG~~G~rIk~i~el~gekIdVVeys~D~~--------------------~fI~N~l~PA~V~~V~i 93 (141)
T TIGR01952 34 RVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENLE--------------------EFVANKLAPAEVKNVTV 93 (141)
T ss_pred EEEEEEcCCCccccCCCCchHHHHHHHhcCCeeEEEEcCCCHH--------------------HHHHHcCCCceEEEEEE
Confidence 5557789999999999999999999988888887764221110 0111100 00100000
Q ss_pred cCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEe
Q 007603 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLV 402 (596)
Q Consensus 353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~ 402 (596)
. ..+....+.+.||.+..+..|||+|++++...+.+|-++.|.
T Consensus 94 ~-------~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI~ 136 (141)
T TIGR01952 94 S-------EFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDID 136 (141)
T ss_pred E-------cCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCCe
Confidence 0 012335788999999999999999999999999999998775
No 47
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.94 E-value=0.0029 Score=68.14 Aligned_cols=73 Identities=19% Similarity=0.259 Sum_probs=58.5
Q ss_pred ceEEEEEecc------ceeeeeeecCchhhhhhccccccEEEecCC-------------CCCCC-CCCcEEEEeec-HHH
Q 007603 128 VAYCGLLANT------TKIGVVVGKGGRNVTRMRIESGAKIVMLPP-------------PACAA-IDDQLIQITGA-TLA 186 (596)
Q Consensus 128 ~vt~rllVp~------~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~-------------p~~~~-~~dRiV~I~G~-~e~ 186 (596)
.++-|+.||- +.+|+|||..|.+.|+|+++|||+|.|..+ ...+. ..+=-|.|+++ -|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 6777888886 579999999999999999999999999873 01111 23335778886 899
Q ss_pred HHHHHHHHHHHHhc
Q 007603 187 VKKALVAVTTCLQH 200 (596)
Q Consensus 187 V~~A~~~I~~~L~e 200 (596)
|.+|+..|..+|++
T Consensus 217 i~~Ai~vienli~~ 230 (554)
T KOG0119|consen 217 IKKAIAVIENLIQS 230 (554)
T ss_pred HHHHHHHHHHHHHh
Confidence 99999999999986
No 48
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.67 E-value=0.0038 Score=60.58 Aligned_cols=101 Identities=19% Similarity=0.249 Sum_probs=66.6
Q ss_pred EEEeccCccceeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHH
Q 007603 28 RLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIR 107 (596)
Q Consensus 28 rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~ 107 (596)
-..+-.+.+|..||++|++|+.|.++.|-+|+|=...++ +.. ...+||.-
T Consensus 79 ~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s~d-----------~~~-------------------fI~nal~P 128 (190)
T COG0195 79 SNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWSED-----------PAE-------------------FIKNALAP 128 (190)
T ss_pred EeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeCCC-----------HHH-------------------HHHHhcCc
Confidence 334445778999999999999999999977776432111 100 01111110
Q ss_pred HHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecC
Q 007603 108 VFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (596)
Q Consensus 108 i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~ 166 (596)
.++...... ..+.. ...+.||..+.+..|||+|.+++.+.+-||-++.|..
T Consensus 129 --a~v~~V~~~-----~~d~~-~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~ 179 (190)
T COG0195 129 --AEVLSVNIK-----EDDGH-VAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIET 179 (190)
T ss_pred --ceEeEEEEE-----eCCCc-EEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEe
Confidence 000000000 00112 7788899999999999999999999999999999965
No 49
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.53 E-value=0.0033 Score=73.69 Aligned_cols=95 Identities=14% Similarity=0.199 Sum_probs=71.7
Q ss_pred ccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccE-EEecCCCCCCCCCCc
Q 007603 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAK-IVMLPPPACAAIDDQ 176 (596)
Q Consensus 98 ~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~-I~I~~~p~~~~~~dR 176 (596)
+..|.++...++..+.+.....-..-....+....+-||.+.++.|||.||.+||.|.++||++ |.+.. +-
T Consensus 654 L~~A~~g~~~Il~~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d--------dg 725 (891)
T PLN00207 654 LLQAKDGRKHILAEMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD--------DG 725 (891)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC--------Ce
Confidence 3456666667766655543222111223336677889999999999999999999999999999 88854 46
Q ss_pred EEEEeec-HHHHHHHHHHHHHHHhc
Q 007603 177 LIQITGA-TLAVKKALVAVTTCLQH 200 (596)
Q Consensus 177 iV~I~G~-~e~V~~A~~~I~~~L~e 200 (596)
.|.|.+. .+++.+|+.+|..++.+
T Consensus 726 ~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 726 TVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred eEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 7888884 99999999999999864
No 50
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.51 E-value=0.005 Score=69.27 Aligned_cols=99 Identities=13% Similarity=0.154 Sum_probs=74.0
Q ss_pred chHHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCC
Q 007603 334 SPVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQ 413 (596)
Q Consensus 334 ~~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~ 413 (596)
.+|..|-++|+..|.+..... . ........-..++.|+.+.++-+||++|++||+|.++|||.|+|.+
T Consensus 522 ~QAk~aRlhIL~~M~~ai~~p-r-~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied---------- 589 (692)
T COG1185 522 EQAKGARLHILIVMNEAISEP-R-KELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED---------- 589 (692)
T ss_pred HHHHHHHHHHHHHHHHHHhhh-h-hhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC----------
Confidence 345566677777775431110 0 0111234568889999999999999999999999999999999962
Q ss_pred CCcEEEEcCCH-HHHHHHHHHHHHHHhhccccc
Q 007603 414 NDVVIQISGEY-KNVQNALSEVVGRLRHNLKSG 445 (596)
Q Consensus 414 ~er~V~I~G~~-~~V~~A~~~I~~~Lr~~~~~~ 445 (596)
+-.|.|.++. +.++.|+..|.+.+++..+..
T Consensus 590 -dGtv~i~~s~~~~~~~ak~~I~~i~~e~evg~ 621 (692)
T COG1185 590 -DGTVKIAASDGESAKKAKERIEAITREVEVGE 621 (692)
T ss_pred -CCcEEEEecchHHHHHHHHHHHHHHhhccccc
Confidence 4669999987 689999999999998766543
No 51
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=96.51 E-value=0.0049 Score=72.28 Aligned_cols=92 Identities=14% Similarity=0.181 Sum_probs=67.8
Q ss_pred HHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCe-EEEeCCCcccccCCCC
Q 007603 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTD-IKLVGGEQVLGCAAQN 414 (596)
Q Consensus 336 a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~-I~I~~~~~~P~~~~~~ 414 (596)
+.++...|++.|.+..... . ............+.||.++++.|||.||.+||+|+++||+. |.+.+
T Consensus 657 A~~g~~~Il~~M~~~i~~p-r-~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~d----------- 723 (891)
T PLN00207 657 AKDGRKHILAEMSKCSPPP-S-KRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQD----------- 723 (891)
T ss_pred HHHHHHHHHHHHHHHHhhh-h-hhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCC-----------
Confidence 4455556666664431110 0 01123456789999999999999999999999999999999 87743
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007603 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 415 er~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (596)
+-.|.|.+ +.+.+++|+.+|.+...+
T Consensus 724 dg~V~I~a~d~~~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 724 DGTVKITAKDLSSLEKSKAIISSLTMV 750 (891)
T ss_pred CeeEEEEeCCHHHHHHHHHHHHHHhcC
Confidence 56788888 577899999999887664
No 52
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.48 E-value=0.0028 Score=63.54 Aligned_cols=40 Identities=20% Similarity=0.500 Sum_probs=36.1
Q ss_pred CCcEEEEEEeccC------ccceeecCCChHHHHHHHHhCceEEEe
Q 007603 22 DDVVSFRLVCPTP------VVGGLIGRSGSIISSIRRDTKCRIHCE 61 (596)
Q Consensus 22 ~~~~~~rilvP~~------~vg~IIGk~G~~Ik~Ir~eTga~I~V~ 61 (596)
+-.++.||+||.+ +||.|+|.+|.++|+|+++|||+|-|-
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~Ir 134 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIR 134 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEe
Confidence 3366889999996 799999999999999999999999984
No 53
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.46 E-value=0.0091 Score=67.26 Aligned_cols=95 Identities=20% Similarity=0.240 Sum_probs=70.5
Q ss_pred ccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcE
Q 007603 98 VSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQL 177 (596)
Q Consensus 98 ~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRi 177 (596)
...|..|-++++..+.+.-.........-.+-...+-++...+.-+||++|++|++|.++|||+|.|.. +..
T Consensus 521 L~QAk~aRlhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--------dGt 592 (692)
T COG1185 521 LEQAKGARLHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--------DGT 592 (692)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC--------CCc
Confidence 345666666776665554322211111122345567789999999999999999999999999999964 567
Q ss_pred EEEeec-HHHHHHHHHHHHHHHhc
Q 007603 178 IQITGA-TLAVKKALVAVTTCLQH 200 (596)
Q Consensus 178 V~I~G~-~e~V~~A~~~I~~~L~e 200 (596)
|.|.+. .+.+.+|+..|..+.++
T Consensus 593 v~i~~s~~~~~~~ak~~I~~i~~e 616 (692)
T COG1185 593 VKIAASDGESAKKAKERIEAITRE 616 (692)
T ss_pred EEEEecchHHHHHHHHHHHHHHhh
Confidence 889887 69999999999999976
No 54
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=96.39 E-value=0.0077 Score=64.95 Aligned_cols=78 Identities=17% Similarity=0.330 Sum_probs=59.0
Q ss_pred ceEEEEEecc------ccccccccCCCchhHHHHHHhCCeEEEeCCC---------ccccc--CCCCCcEEEEcCC-HHH
Q 007603 365 AVAVSILVGA------DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE---------QVLGC--AAQNDVVIQISGE-YKN 426 (596)
Q Consensus 365 ~~t~~l~VP~------~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~---------~~P~~--~~~~er~V~I~G~-~~~ 426 (596)
..+.+|.||- ++||.|||..|.+.|+|.++|||+|.|-.+. +.+.+ ..+++--+.|+.+ .|.
T Consensus 137 ~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk~~~~d~~~~~~~~epLH~~Isadt~ek 216 (554)
T KOG0119|consen 137 KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGKGRSDDLSYIPKENEPLHCLISADTQEK 216 (554)
T ss_pred ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccccCCcccccccccccceeEEEecchHHH
Confidence 5677888874 5899999999999999999999999997621 11111 1344556777776 558
Q ss_pred HHHHHHHHHHHHhhcc
Q 007603 427 VQNALSEVVGRLRHNL 442 (596)
Q Consensus 427 V~~A~~~I~~~Lr~~~ 442 (596)
|++|..+|...|.+..
T Consensus 217 i~~Ai~vienli~~av 232 (554)
T KOG0119|consen 217 IKKAIAVIENLIQSAV 232 (554)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999999888633
No 55
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.38 E-value=0.003 Score=66.78 Aligned_cols=65 Identities=18% Similarity=0.312 Sum_probs=54.3
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHH
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRL 438 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~L 438 (596)
...-+.|.+++||.+||++|++|+.||..|.++|+|.+.+ .+..|+|.|..+--.+|+..|..-+
T Consensus 47 ~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~~~--------~e~kv~ifg~~~m~~kaka~id~~~ 111 (629)
T KOG0336|consen 47 FPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIKCD--------LEVKVTIFGINHMRKKAKASIDRGQ 111 (629)
T ss_pred CchhhhhhhhhhheeeccCcchhhhhhcccceeEEEeccC--------ceeEEEEechHHHHHHHHhhHhhhh
Confidence 4556677889999999999999999999999999998743 4788999999887777777765433
No 56
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=96.38 E-value=0.0031 Score=64.96 Aligned_cols=70 Identities=19% Similarity=0.259 Sum_probs=58.0
Q ss_pred ceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEE-eecHHHHHHHHHHHHHHHhcc
Q 007603 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI-TGATLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 128 ~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I-~G~~e~V~~A~~~I~~~L~e~ 201 (596)
....-++|+.+..++|||++|.+-++|+++|+++|.++. +......|.| .+..++|.+|...|...|.+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~----p~~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPR----PNTNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccC----CCCCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 345568999999999999999999999999999999987 3433444445 456999999999999999774
No 57
>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=96.36 E-value=0.0053 Score=48.46 Aligned_cols=37 Identities=22% Similarity=0.261 Sum_probs=34.4
Q ss_pred cEEEEEEeccCccceeecCCChHHHHHHHHhCceEEE
Q 007603 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (596)
Q Consensus 24 ~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V 60 (596)
.-.+.+.|+.+..|.+|||+|.+|+.+++.++.+|.|
T Consensus 24 ~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 24 EKRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred CcEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 4688899999999999999999999999999988876
No 58
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=96.32 E-value=0.021 Score=57.44 Aligned_cols=82 Identities=20% Similarity=0.287 Sum_probs=59.1
Q ss_pred CCceEEEEEeccc------cccccccCCCchhHHHHHHhCCeEEEeCCCc------------ccccC---CCCCcEEEEc
Q 007603 363 GDAVAVSILVGAD------FVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ------------VLGCA---AQNDVVIQIS 421 (596)
Q Consensus 363 ~~~~t~~l~VP~~------~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~------------~P~~~---~~~er~V~I~ 421 (596)
....+.+|+||-+ +||+|+|..|.++|+++++|||+|-|-.+.- .|+|+ ..-..+|+..
T Consensus 89 ~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD~~KEE~lR~~p~yeHL~epLHVlIe~~ 168 (259)
T KOG1588|consen 89 PVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRDKAKEEELRGDPGYEHLNEPLHVLIETE 168 (259)
T ss_pred ceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccchHHHHHhhcCcchHHhCCCcEEEEEEe
Confidence 4568889998864 9999999999999999999999999976533 23332 2224677888
Q ss_pred CCHHHHHHHHHHHHHHHhhcccc
Q 007603 422 GEYKNVQNALSEVVGRLRHNLKS 444 (596)
Q Consensus 422 G~~~~V~~A~~~I~~~Lr~~~~~ 444 (596)
.++..+..=+..-.+.|+++|+.
T Consensus 169 ~p~~ea~~rl~~AleeI~klL~P 191 (259)
T KOG1588|consen 169 APPAEAYARLAYALEEIKKLLVP 191 (259)
T ss_pred CCHHHHHHHHHHHHHHHHHhcCC
Confidence 88877666444444555555543
No 59
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=96.27 E-value=0.0048 Score=65.33 Aligned_cols=72 Identities=18% Similarity=0.300 Sum_probs=58.9
Q ss_pred CCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHh
Q 007603 123 GDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQ 199 (596)
Q Consensus 123 ~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~ 199 (596)
..+.....+.+-+-+++||.+||++|++|+.|+..|+++|+|.+ ...+-.|+|-|...--.+|...|-..+.
T Consensus 41 aag~~e~plcf~iks~mvg~vigrggskik~iq~~tnt~iqii~-----~~~e~kv~ifg~~~m~~kaka~id~~~~ 112 (629)
T KOG0336|consen 41 AAGGGEFPLCFSIKSEMVGKVIGRGGSKIKRIQNDTNTRIQIIK-----CDLEVKVTIFGINHMRKKAKASIDRGQD 112 (629)
T ss_pred ccCCCCCchhhhhhhhhhheeeccCcchhhhhhcccceeEEEec-----cCceeEEEEechHHHHHHHHhhHhhhhh
Confidence 34566788889999999999999999999999999999999977 2356788999987766666666655543
No 60
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=96.14 E-value=0.0037 Score=60.68 Aligned_cols=102 Identities=21% Similarity=0.238 Sum_probs=69.6
Q ss_pred EEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHh--hhhhccc
Q 007603 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFA--RSVEVEG 352 (596)
Q Consensus 275 ~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~--~i~e~~~ 352 (596)
.+...+-.+.+|..||++|.+|+.|+++.|=+|.|-.-. + .++ .-+..++. ++.....
T Consensus 77 v~~~~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~s-------------~------d~~-~fI~nal~Pa~v~~V~~ 136 (190)
T COG0195 77 VVSNVVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEWS-------------E------DPA-EFIKNALAPAEVLSVNI 136 (190)
T ss_pred eEEeecCcCchhhhccCCChHHHHHHHHhCCceEEEEeC-------------C------CHH-HHHHHhcCcceEeEEEE
Confidence 344556678899999999999999999999666655321 1 111 11112111 1100000
Q ss_pred cCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCC
Q 007603 353 QQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (596)
Q Consensus 353 ~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (596)
.......+.+.||.++.+..|||+|.+++...+.||-+|.|...
T Consensus 137 --------~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg~~i~I~~~ 180 (190)
T COG0195 137 --------KEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTGWEIDIETI 180 (190)
T ss_pred --------EeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhCCEEEEEeh
Confidence 00012278899999999999999999999999999999999763
No 61
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.08 E-value=0.011 Score=62.65 Aligned_cols=95 Identities=21% Similarity=0.269 Sum_probs=63.5
Q ss_pred CccceeecCCChHHHHHHHHh-CceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007603 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (596)
Q Consensus 34 ~~vg~IIGk~G~~Ik~Ir~eT-ga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (596)
+-+|+.||++|++|+.|.++. |-+|.|-....+..+ . +.+| ++||. +
T Consensus 243 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~---f-------i~na-------------l~Pa~---------v 290 (341)
T TIGR01953 243 DPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE---F-------IANA-------------LSPAK---------V 290 (341)
T ss_pred CcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------cCCce---------E
Confidence 468999999999999999999 778887432111000 0 0000 11110 0
Q ss_pred HhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecC
Q 007603 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (596)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~ 166 (596)
....... ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..
T Consensus 291 ~~v~i~~------~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s 338 (341)
T TIGR01953 291 ISVEVLD------EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKT 338 (341)
T ss_pred EEEEEEc------CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEe
Confidence 0000000 01246789999999999999999999999999999999965
No 62
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.97 E-value=0.014 Score=62.35 Aligned_cols=96 Identities=17% Similarity=0.253 Sum_probs=64.2
Q ss_pred CccceeecCCChHHHHHHHHh-CceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007603 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (596)
Q Consensus 34 ~~vg~IIGk~G~~Ik~Ir~eT-ga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (596)
+-+|+.||++|++|+.|.++. |-+|.|=....+..+ . +.+| ++||. +.
T Consensus 245 DpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~---f-------i~na-------------l~Pa~--v~------ 293 (362)
T PRK12327 245 DAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAE---F-------VANA-------------LSPAK--VV------ 293 (362)
T ss_pred CchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------CCCce--EE------
Confidence 568999999999999999999 778887432111000 0 0000 11110 00
Q ss_pred HhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCC
Q 007603 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (596)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~ 167 (596)
..... + ...-.+.+.||..+.+..|||+|.|++....-||.+|.|...
T Consensus 294 -~v~i~-~-----~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~ 341 (362)
T PRK12327 294 -SVEVD-D-----EEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSE 341 (362)
T ss_pred -EEEEE-c-----CCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEH
Confidence 00000 0 113467899999999999999999999999999999999763
No 63
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=95.94 E-value=0.011 Score=63.88 Aligned_cols=95 Identities=23% Similarity=0.260 Sum_probs=63.2
Q ss_pred CccceeecCCChHHHHHHHHh-CceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007603 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (596)
Q Consensus 34 ~~vg~IIGk~G~~Ik~Ir~eT-ga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (596)
+-+|+.||++|++|+.|.++. |-+|.|=....+.. ..| .+| ++|| ++
T Consensus 277 DPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~---~fI-------~Na-------------LsPA---------~V 324 (449)
T PRK12329 277 DPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA---TYI-------ANA-------------LSPA---------RV 324 (449)
T ss_pred ChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH---HHH-------HHh-------------cCCc---------ee
Confidence 568999999999999999999 77888743211100 000 000 1111 00
Q ss_pred HhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecC
Q 007603 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (596)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~ 166 (596)
....... ...-.+.+.||..+.+..|||+|.|++....-||.+|.|..
T Consensus 325 ~~V~i~~------~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 325 DEVRLVD------PEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred eEEEEEc------CCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0000000 01235679999999999999999999999999999999966
No 64
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.87 E-value=0.014 Score=62.25 Aligned_cols=95 Identities=16% Similarity=0.214 Sum_probs=64.0
Q ss_pred CccceeecCCChHHHHHHHHh-CceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007603 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (596)
Q Consensus 34 ~~vg~IIGk~G~~Ik~Ir~eT-ga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (596)
+-+|+.||++|++|+.|.++. |-+|+|-....+..+ . +.+| ++||. +..+
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~---f-------I~Na-------------l~Pa~--V~~V---- 301 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEI---F-------IARA-------------LAPAI--ISSV---- 301 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHH---H-------HHHh-------------CCCce--eeEE----
Confidence 458999999999999999999 778877432111100 0 0000 11110 0000
Q ss_pred HhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCC
Q 007603 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (596)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~ 167 (596)
.. + ...-.+.+.||..+.+..|||+|.+++....-||.+|.|..-
T Consensus 302 ---~i--~-----~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~ 346 (374)
T PRK12328 302 ---KI--E-----EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEI 346 (374)
T ss_pred ---EE--c-----CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEEC
Confidence 00 0 113467889999999999999999999999999999999864
No 65
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=95.83 E-value=0.012 Score=60.72 Aligned_cols=71 Identities=24% Similarity=0.315 Sum_probs=59.7
Q ss_pred ceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007603 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (596)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (596)
.....+.|++.+.|.|||++|.+.+.|.++|+++|.++.+. ...+.++.+-+..++|..|...|...|-+.
T Consensus 56 ~~~~si~v~s~~~~~lig~~g~trkkle~Etq~~i~lp~p~------~n~~~i~i~~~~~~~V~~a~~Ri~~~ids~ 126 (345)
T KOG2814|consen 56 DFSSSILVRSSFIGWLIGKQGKTRKKLEEETQTNIFLPRPN------TNKEEIKIIGISRNCVIQALERIAKLIDSD 126 (345)
T ss_pred cchhhhhhhHHHhhhhhcccchHHHHHHHhhccceEccCCC------CCcceEEEeehhHHHHHHHHHHHHHHHHhh
Confidence 45778899999999999999999999999999999998743 245666667777889999999998766653
No 66
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.77 E-value=0.013 Score=46.25 Aligned_cols=36 Identities=22% Similarity=0.372 Sum_probs=34.1
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEE
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL 401 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I 401 (596)
....+.|+.+..|..|||+|.+|+.+++.+|-+|.|
T Consensus 25 ~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPDDQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECcccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 688999999999999999999999999999998876
No 67
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.48 E-value=0.022 Score=66.31 Aligned_cols=93 Identities=14% Similarity=0.217 Sum_probs=65.8
Q ss_pred hHHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCC
Q 007603 335 PVQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQN 414 (596)
Q Consensus 335 ~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~ 414 (596)
.+.++...|++.|.+..... .. ...........+.||.+.++.+||.||.+||+|+++||+.|.+.+
T Consensus 525 ~a~~g~~~I~~~M~~aI~~~-r~-~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d----------- 591 (693)
T PRK11824 525 QAKEGRLHILGKMNEAISEP-RA-ELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED----------- 591 (693)
T ss_pred HHHHHHHHHHHHHHHHhcCC-hh-hhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC-----------
Confidence 34455566676665432111 00 011234456788889999999999999999999999999887632
Q ss_pred CcEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007603 415 DVVIQISG-EYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 415 er~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (596)
+-.|.|.+ ..+.+++|+.+|.....+
T Consensus 592 ~G~v~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 592 DGTVKIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred CceEEEEcccHHHHHHHHHHHHHhccc
Confidence 56688888 477899999999876653
No 68
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.44 E-value=0.027 Score=56.88 Aligned_cols=64 Identities=19% Similarity=0.180 Sum_probs=54.8
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHH-HHHHHHHHHHHHHhhc
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK-NVQNALSEVVGRLRHN 441 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~-~V~~A~~~I~~~Lr~~ 441 (596)
-..+.||.++++.+||++|.+|+.|.+.|++.|.|-. +-.|.|+++.. ++..|+.+|...-++.
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 4678899999999999999999999999999998843 57799999865 8889999998765543
No 69
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=95.38 E-value=0.015 Score=67.52 Aligned_cols=94 Identities=20% Similarity=0.242 Sum_probs=67.0
Q ss_pred cHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEE
Q 007603 99 SSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLI 178 (596)
Q Consensus 99 ~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV 178 (596)
..|.++..+|++.+.+.....-.+-....+....+-|+.+.++.+||+||.+||+|.++||++|.+.. +-.|
T Consensus 524 ~~a~~g~~~I~~~M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--------~G~v 595 (693)
T PRK11824 524 EQAKEGRLHILGKMNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--------DGTV 595 (693)
T ss_pred HHHHHHHHHHHHHHHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC--------CceE
Confidence 44556666666665554322111111122344556679999999999999999999999999888743 5678
Q ss_pred EEee-cHHHHHHHHHHHHHHHhc
Q 007603 179 QITG-ATLAVKKALVAVTTCLQH 200 (596)
Q Consensus 179 ~I~G-~~e~V~~A~~~I~~~L~e 200 (596)
.|.+ ..+++.+|..+|..+..+
T Consensus 596 ~i~~~~~~~~~~a~~~I~~~~~~ 618 (693)
T PRK11824 596 KIAATDGEAAEAAKERIEGITAE 618 (693)
T ss_pred EEEcccHHHHHHHHHHHHHhccc
Confidence 8888 499999999999888754
No 70
>PRK00468 hypothetical protein; Provisional
Probab=95.27 E-value=0.021 Score=47.09 Aligned_cols=35 Identities=29% Similarity=0.442 Sum_probs=31.0
Q ss_pred CCCcEEEEEEeccCccceeecCCChHHHHHHHHhC
Q 007603 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (596)
Q Consensus 21 ~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTg 55 (596)
.++.+.+++-|..+..|.||||+|.+|+.||.--.
T Consensus 26 ~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 26 GEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 45668999999999999999999999999997653
No 71
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=95.21 E-value=0.015 Score=61.74 Aligned_cols=97 Identities=19% Similarity=0.264 Sum_probs=64.2
Q ss_pred cccccccccccchhhhhhhhcc-CeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCCCCC
Q 007603 282 GWTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGE 360 (596)
Q Consensus 282 ~~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~ 360 (596)
-+-+|..||++|.+|+.|.++. |=+|.|-.-..+..+ +.. +.++|+ ++......
T Consensus 242 iDpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~--fi~-------nal~Pa---------~v~~v~i~------- 296 (341)
T TIGR01953 242 IDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAE--FIA-------NALSPA---------KVISVEVL------- 296 (341)
T ss_pred CCcceeeECCCCchHHHHHHHhCCCeEEEEEcCCCHHH--HHH-------HhcCCc---------eEEEEEEE-------
Confidence 3567999999999999999988 666766532211100 000 000111 00000000
Q ss_pred CCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCC
Q 007603 361 NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (596)
Q Consensus 361 ~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (596)
. .......+.||.++.+..|||+|.+++...+.||.+|.|.+.
T Consensus 297 ~-~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~l~g~~IdI~s~ 339 (341)
T TIGR01953 297 D-EDKHSAEVVVPDDQLSLAIGKGGQNVRLASKLTGWNIDVKTE 339 (341)
T ss_pred c-CCCcEEEEEEChHHcchhhcCCChhHHHHHHHhCCEEEEEeC
Confidence 0 122478999999999999999999999999999999999763
No 72
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=95.02 E-value=0.035 Score=61.39 Aligned_cols=94 Identities=20% Similarity=0.276 Sum_probs=62.8
Q ss_pred CccceeecCCChHHHHHHHHh-CceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHHHHHHH
Q 007603 34 PVVGGLIGRSGSIISSIRRDT-KCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERM 112 (596)
Q Consensus 34 ~~vg~IIGk~G~~Ik~Ir~eT-ga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i 112 (596)
+-+|+.||++|++|+.|.++. |-+|.|-...++. ...|. ++ ++|| .+
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~---~~fi~-------na-------------l~pa---------~v 292 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDP---AQFII-------NA-------------LSPA---------EV 292 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCH---HHHHH-------Hh-------------CCCC---------EE
Confidence 458999999999999999999 7788774321110 00000 00 0010 00
Q ss_pred HhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecC
Q 007603 113 WEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLP 166 (596)
Q Consensus 113 ~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~ 166 (596)
..... +. ..-.+.+.||..+.+..|||+|.+|+..+.-||.+|.|..
T Consensus 293 ~~v~~--~~-----~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~ 339 (470)
T PRK09202 293 SSVVV--DE-----DEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMT 339 (470)
T ss_pred EEEEE--eC-----CCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEE
Confidence 00000 00 0236779999999999999999999999999999999976
No 73
>PRK02821 hypothetical protein; Provisional
Probab=94.72 E-value=0.033 Score=46.07 Aligned_cols=36 Identities=17% Similarity=0.272 Sum_probs=31.4
Q ss_pred CCCcEEEEEEeccCccceeecCCChHHHHHHHHhCc
Q 007603 21 PDDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (596)
Q Consensus 21 ~~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga 56 (596)
.++.+.++|-|....+|.||||+|.+|+.||.--.+
T Consensus 27 ~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a 62 (77)
T PRK02821 27 NRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAA 62 (77)
T ss_pred CCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHH
Confidence 345688999999999999999999999999987654
No 74
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=94.69 E-value=0.021 Score=60.81 Aligned_cols=98 Identities=12% Similarity=0.072 Sum_probs=66.0
Q ss_pred ccccccccccchhhhhhhhcc-CeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCCCCCC
Q 007603 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (596)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~~ 361 (596)
+-+|..||++|.+|+.|.++. |=+|.|-.-..+..+-+ . +.++|+ ++..... .
T Consensus 251 DPvGacIG~~G~rI~~I~~eL~gEkIDvI~~s~D~~~fI--~-------Nal~Pa---------~V~~V~i--------~ 304 (374)
T PRK12328 251 DPIGATVGVKGVRINAVSKELNGENIDCIEYSNVPEIFI--A-------RALAPA---------IISSVKI--------E 304 (374)
T ss_pred ChHHhhcCCCcchHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhCCCc---------eeeEEEE--------c
Confidence 567999999999999999988 76676653221110000 0 000111 0000000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcc
Q 007603 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV 407 (596)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~ 407 (596)
+......+.||.++.+..|||+|++++.-.+.||.+|.|.+-+..
T Consensus 305 -~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~LtGwkIDI~s~~~~ 349 (374)
T PRK12328 305 -EEEKKAIVTLLSDQKSKAIGKNGINIRLASMLTGYEIELNEIGSK 349 (374)
T ss_pred -CCCcEEEEEEChHHhhhhhcCCChhHHHHHHHhCCEEEEEECCCC
Confidence 123478999999999999999999999999999999999986653
No 75
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.38 E-value=0.023 Score=60.75 Aligned_cols=98 Identities=18% Similarity=0.196 Sum_probs=65.0
Q ss_pred cccccccccccchhhhhhhhcc-CeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCCCCC
Q 007603 282 GWTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGE 360 (596)
Q Consensus 282 ~~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~ 360 (596)
-+-+|..||++|.+|+.|.++. |-+|.|-.-..+..+-+ . +.++|| ++.....
T Consensus 244 iDpvGa~iG~~G~rI~~i~~el~gekIdiv~~s~d~~~fi--~-------nal~Pa---------~v~~v~i-------- 297 (362)
T PRK12327 244 VDAKGACVGPKGQRVQNIVSELKGEKIDIIDWSEDPAEFV--A-------NALSPA---------KVVSVEV-------- 297 (362)
T ss_pred CCchheeECCCChhHHHHHHHhCCCeEEEEEcCCCHHHHH--H-------HhCCCc---------eEEEEEE--------
Confidence 3568999999999999999988 77776653221110000 0 000110 0000000
Q ss_pred CCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCC
Q 007603 361 NKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE 405 (596)
Q Consensus 361 ~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~ 405 (596)
..+......+.||.++.+.-|||+|.+++.-.+.||.+|.|.+.+
T Consensus 298 ~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L~~~~idi~s~~ 342 (362)
T PRK12327 298 DDEEEKAARVVVPDYQLSLAIGKEGQNARLAARLTGWKIDIKSES 342 (362)
T ss_pred EcCCCcEEEEEEChhhcchhhcCCChhHHHHHHHHCCeeeEEEHH
Confidence 001234789999999999999999999999999999999998643
No 76
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=94.28 E-value=0.14 Score=49.51 Aligned_cols=41 Identities=27% Similarity=0.459 Sum_probs=34.7
Q ss_pred CcEEEEEEecc------CccceeecCCChHHHHHHHHhCceEEEeCC
Q 007603 23 DVVSFRLVCPT------PVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (596)
Q Consensus 23 ~~~~~rilvP~------~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~ 63 (596)
-.+.=++.||. .++|.|||..|+|.|+|++.|+|+|-|.-.
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 34556677776 589999999999999999999999999643
No 77
>PRK12704 phosphodiesterase; Provisional
Probab=94.17 E-value=0.12 Score=58.07 Aligned_cols=68 Identities=13% Similarity=0.227 Sum_probs=51.6
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHHhhc
Q 007603 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRLRHN 441 (596)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~Lr~~ 441 (596)
..++..+.+|+ ++-|+|||+.|.+|+-+...||++|.|++ +...|.|+| .|---+.|...+...+.++
T Consensus 208 e~~~~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~~~~~rre~a~~~l~~l~~dg 277 (520)
T PRK12704 208 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPIRREIARLALEKLVQDG 277 (520)
T ss_pred hhceeeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC----------CCCeEEEecCChhhHHHHHHHHHHHHhcC
Confidence 34566788888 79999999999999999999999999964 346778998 4555455655555544443
No 78
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=94.07 E-value=0.057 Score=44.42 Aligned_cols=54 Identities=20% Similarity=0.371 Sum_probs=37.2
Q ss_pred HHHHHHHHHHhhhhccC-CCCCCCCceEEEEEeccceeeeeeecCchhhhhhccc
Q 007603 104 AVIRVFERMWEVEAEVE-GDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (596)
Q Consensus 104 Al~~i~~~i~~~~~~~~-~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~e 157 (596)
.+..+...+++..++-. .....+..+.++|-+.....|.||||+|.+|+.||.-
T Consensus 4 lv~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 4 LVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred HHHHHHHHhcCCccceEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHHH
Confidence 34455555554432210 0012355788999999999999999999999999954
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.07 E-value=0.13 Score=55.81 Aligned_cols=94 Identities=20% Similarity=0.182 Sum_probs=63.2
Q ss_pred cccccccccccchhhhhhhhcc-CeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHH--hhhhhccccCCCCC
Q 007603 282 GWTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVF--ARSVEVEGQQGFSS 358 (596)
Q Consensus 282 ~~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~--~~i~e~~~~~g~~~ 358 (596)
.+-+|..||++|.+|+.|.++. |=+|.|-.-..+.. .-+...+ .++.....
T Consensus 276 VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ys~Dp~--------------------~fI~NaLsPA~V~~V~i------ 329 (449)
T PRK12329 276 VDPVGACIGARGSRIQAVVNELRGEKIDVIRWSPDPA--------------------TYIANALSPARVDEVRL------ 329 (449)
T ss_pred CChhhccCCCCcchHHHHHHHhCCCeEEEEEcCCCHH--------------------HHHHHhcCCceeeEEEE------
Confidence 3568999999999999999998 66666653211110 0111000 01100000
Q ss_pred CCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeC
Q 007603 359 GENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (596)
Q Consensus 359 g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~ 403 (596)
.........+.||.++.+.-|||+|.+++.-.+.||.+|.|.+
T Consensus 330 --~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~Ltg~~idI~s 372 (449)
T PRK12329 330 --VDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAARLTGWKIDIKD 372 (449)
T ss_pred --EcCCCcEEEEEEChHhcchhhcCCChhHHHHHHHHCCEecccc
Confidence 0012246789999999999999999999999999999999975
No 80
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=94.02 E-value=1.4 Score=43.56 Aligned_cols=86 Identities=19% Similarity=0.317 Sum_probs=65.5
Q ss_pred HHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeec
Q 007603 104 AVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA 183 (596)
Q Consensus 104 Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~ 183 (596)
.+.+|++.+........- +..-.+.+-++....-.|+..+|..++.|....||+|.+.. .+..|.|+|+
T Consensus 5 l~~~Il~d~W~l~v~e~v----~~~g~l~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~-------~~~~i~I~g~ 73 (210)
T PF14611_consen 5 LAERILRDCWNLEVSEEV----DELGDLDVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSR-------SENRIRITGT 73 (210)
T ss_pred HHHHHHHHhcCCccccee----eccceeEEEecchheeeeecCCchHHHHHHHhcCceEEEec-------CCcEEEEEcc
Confidence 455677776665433211 11223344456888899999999999999888999999987 5678999999
Q ss_pred HHHHHHHHHHHHHHHhc
Q 007603 184 TLAVKKALVAVTTCLQH 200 (596)
Q Consensus 184 ~e~V~~A~~~I~~~L~e 200 (596)
...+..+...|.+++..
T Consensus 74 k~~~~~i~~~i~~~l~~ 90 (210)
T PF14611_consen 74 KSTAEYIEASINEILSN 90 (210)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 99999999999999976
No 81
>PRK01064 hypothetical protein; Provisional
Probab=93.98 E-value=0.068 Score=44.35 Aligned_cols=34 Identities=26% Similarity=0.527 Sum_probs=30.8
Q ss_pred CCcEEEEEEeccCccceeecCCChHHHHHHHHhC
Q 007603 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (596)
Q Consensus 22 ~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTg 55 (596)
++.+.+++-|.....|.+|||+|.+|+.||.-..
T Consensus 27 ~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 27 THTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred CCEEEEEEEECcccceEEECCCCccHHHHHHHHH
Confidence 5678999999999999999999999999998653
No 82
>PRK00468 hypothetical protein; Provisional
Probab=93.90 E-value=0.063 Score=44.22 Aligned_cols=34 Identities=15% Similarity=0.257 Sum_probs=29.6
Q ss_pred CCceEEEEEeccccccccccCCCchhHHHHHHhC
Q 007603 363 GDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTG 396 (596)
Q Consensus 363 ~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG 396 (596)
+..+..++.+.++.+|+||||+|.+|+.|+.--.
T Consensus 27 ~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~ 60 (75)
T PRK00468 27 EQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVK 60 (75)
T ss_pred CCeEEEEEEEChhhCcceecCCChhHHHHHHHHH
Confidence 3557889999999999999999999999986543
No 83
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.89 E-value=0.067 Score=44.01 Aligned_cols=33 Identities=27% Similarity=0.458 Sum_probs=30.0
Q ss_pred CCcEEEEEEeccCccceeecCCChHHHHHHHHh
Q 007603 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDT 54 (596)
Q Consensus 22 ~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eT 54 (596)
+..+.++|-+.....|.||||+|.+|+.||.--
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll 59 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLL 59 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHH
Confidence 667889999999999999999999999999754
No 84
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.76 E-value=0.17 Score=56.89 Aligned_cols=65 Identities=14% Similarity=0.237 Sum_probs=49.3
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHH
Q 007603 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRL 438 (596)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~L 438 (596)
..++..+.+|+ ++-|+|||+.|.+|+-+...||++|.|.+ +...|+|+| .|---+.|...+...+
T Consensus 202 e~~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd----------tp~~v~ls~fdp~rreia~~~l~~li 268 (514)
T TIGR03319 202 ETTVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD----------TPEAVILSGFDPVRREIARMALEKLI 268 (514)
T ss_pred hheeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC----------CCCeEEecCCchHHHHHHHHHHHHHH
Confidence 45677788888 89999999999999999999999999964 345677888 4544445544444433
No 85
>PRK02821 hypothetical protein; Provisional
Probab=93.72 E-value=0.087 Score=43.59 Aligned_cols=32 Identities=25% Similarity=0.435 Sum_probs=28.3
Q ss_pred CCceEEEEEeccceeeeeeecCchhhhhhccc
Q 007603 126 DDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (596)
Q Consensus 126 ~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~e 157 (596)
+..+.+.|.|....+|.||||+|.+|+.||.-
T Consensus 28 ~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtl 59 (77)
T PRK02821 28 RRGRTLEVRVHPDDLGKVIGRGGRTATALRTV 59 (77)
T ss_pred CCcEEEEEEEChhhCcceeCCCCchHHHHHHH
Confidence 34578899999999999999999999999965
No 86
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=93.46 E-value=0.042 Score=60.78 Aligned_cols=96 Identities=20% Similarity=0.242 Sum_probs=63.7
Q ss_pred ccccccccccchhhhhhhhcc-CeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCCCCCC
Q 007603 283 WTASGIIGKRGAIVRSLQNAS-GALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGEN 361 (596)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~t-Ga~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~~ 361 (596)
+-+|..||++|.+|+.|.++. |=+|.|-.-.++... + +..|+.- .++..... +
T Consensus 245 Dpvga~vG~~G~ri~~i~~el~ge~Idiv~~s~d~~~--f--------------i~nal~p--a~v~~v~~--------~ 298 (470)
T PRK09202 245 DPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQ--F--------------IINALSP--AEVSSVVV--------D 298 (470)
T ss_pred ChhHccCCCCCchHHHHHHHhCCCeEEEEEcCCCHHH--H--------------HHHhCCC--CEEEEEEE--------e
Confidence 457999999999999999988 666766532111100 0 0001000 00000000 0
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCC
Q 007603 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGE 405 (596)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~ 405 (596)
...-...+.||.++.+.-|||+|++++...+.||.+|.|...+
T Consensus 299 -~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~g~~idi~~~~ 341 (470)
T PRK09202 299 -EDEHSADVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIMTEE 341 (470)
T ss_pred -CCCCEEEEEECcchHHHhhCCCCeeHHHHHHHHCCeEEEEEhh
Confidence 1123889999999999999999999999999999999998743
No 87
>PRK00106 hypothetical protein; Provisional
Probab=93.39 E-value=0.21 Score=56.05 Aligned_cols=65 Identities=15% Similarity=0.273 Sum_probs=49.7
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcC-CHHHHHHHHHHHHHHH
Q 007603 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISG-EYKNVQNALSEVVGRL 438 (596)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G-~~~~V~~A~~~I~~~L 438 (596)
..++..+.+|+ ++-|+|||+.|.+|+-+...||+++.|++ +...|+|+| .|---+.|...+...+
T Consensus 223 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd----------tp~~v~lS~fdpvRReiAr~~le~Li 289 (535)
T PRK00106 223 EQTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD----------TPEVVVLSGFDPIRREIARMTLESLI 289 (535)
T ss_pred hheeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC----------CCCeEEEeCCChHHHHHHHHHHHHHH
Confidence 45677788888 89999999999999999999999999964 345677888 5555555554444433
No 88
>PRK01064 hypothetical protein; Provisional
Probab=93.33 E-value=0.095 Score=43.51 Aligned_cols=33 Identities=27% Similarity=0.503 Sum_probs=29.3
Q ss_pred CCCceEEEEEeccceeeeeeecCchhhhhhccc
Q 007603 125 GDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (596)
Q Consensus 125 ~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~e 157 (596)
.+..+.+++.|.....|.+|||+|.+|+.||.-
T Consensus 26 ~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l 58 (78)
T PRK01064 26 GTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTL 58 (78)
T ss_pred CCCEEEEEEEECcccceEEECCCCccHHHHHHH
Confidence 345788999999999999999999999999864
No 89
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=93.22 E-value=0.32 Score=47.18 Aligned_cols=42 Identities=24% Similarity=0.460 Sum_probs=36.0
Q ss_pred CCceEEEEEec------cccccccccCCCchhHHHHHHhCCeEEEeCC
Q 007603 363 GDAVAVSILVG------ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (596)
Q Consensus 363 ~~~~t~~l~VP------~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (596)
....+-++.|| .++||.|||..|.+.|++++.|+|+|-|-..
T Consensus 145 psk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~ 192 (269)
T COG5176 145 PSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGS 192 (269)
T ss_pred cccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecc
Confidence 45567777776 4799999999999999999999999999754
No 90
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=93.21 E-value=0.27 Score=55.33 Aligned_cols=65 Identities=15% Similarity=0.305 Sum_probs=49.6
Q ss_pred eEEEEEecc-ceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEee-cHHHHHHHHHHHHHHHhc
Q 007603 129 AYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH 200 (596)
Q Consensus 129 vt~rllVp~-~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G-~~e~V~~A~~~I~~~L~e 200 (596)
....+-+|+ .+-|.||||.|.||+.++.-||+.+.|.. +...|+|+| +|---+-|...+..++.+
T Consensus 204 ~~~~v~lp~d~~kgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~fdp~rreia~~~l~~li~d 270 (514)
T TIGR03319 204 TVSVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPVRREIARMALEKLIQD 270 (514)
T ss_pred eeeeEEcCChhhhccccCCCcchHHHHHHHhCceEEEcC-------CCCeEEecCCchHHHHHHHHHHHHHHHc
Confidence 334455666 88999999999999999999999999976 456788888 455555566666666654
No 91
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=93.18 E-value=0.14 Score=51.60 Aligned_cols=62 Identities=21% Similarity=0.267 Sum_probs=52.9
Q ss_pred EEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhcc
Q 007603 132 GLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 132 rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~-~e~V~~A~~~I~~~L~e~ 201 (596)
.+-||...++.+||++|.+|+.|.++++++|.|-. +-.|.|.+. .+++.+|+.+|..+-++.
T Consensus 148 ~~~V~~~~i~~lig~~g~~i~~l~~~~~~~I~ig~--------NG~VwI~~~~~~~~~~a~~~I~~~e~~~ 210 (235)
T PRK04163 148 IVEIKPVKVPRVIGKKGSMINMLKEETGCDIIVGQ--------NGRIWIKGPDEEDEEIAIEAIKKIEREA 210 (235)
T ss_pred EEEECHHHHHhhcCCCChhHhhhhhhhCcEEEEcC--------CcEEEEeeCCHHHHHHHHHHHHHHHhhh
Confidence 36789999999999999999999999999999954 356888887 678888988888777663
No 92
>PRK00106 hypothetical protein; Provisional
Probab=93.05 E-value=0.32 Score=54.70 Aligned_cols=66 Identities=12% Similarity=0.316 Sum_probs=50.6
Q ss_pred ceEEEEEecc-ceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEee-cHHHHHHHHHHHHHHHhc
Q 007603 128 VAYCGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH 200 (596)
Q Consensus 128 ~vt~rllVp~-~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G-~~e~V~~A~~~I~~~L~e 200 (596)
.....+-+|+ .+-|.||||.|.||+.++.-||+.+.|.. +...|.|+| +|---+-|...+..++.+
T Consensus 224 ~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~v~lS~fdpvRReiAr~~le~Li~d 291 (535)
T PRK00106 224 QTITTVHLPDDNMKGRIIGREGRNIRTLESLTGIDVIIDD-------TPEVVVLSGFDPIRREIARMTLESLIKD 291 (535)
T ss_pred heeeeEEcCChHhhcceeCCCcchHHHHHHHhCceEEEcC-------CCCeEEEeCCChHHHHHHHHHHHHHHHc
Confidence 3344556676 78999999999999999999999999976 456788998 465555566666666654
No 93
>PRK12704 phosphodiesterase; Provisional
Probab=92.88 E-value=0.3 Score=55.02 Aligned_cols=63 Identities=16% Similarity=0.318 Sum_probs=48.8
Q ss_pred EEEEecc-ceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEee-cHHHHHHHHHHHHHHHhc
Q 007603 131 CGLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITG-ATLAVKKALVAVTTCLQH 200 (596)
Q Consensus 131 ~rllVp~-~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G-~~e~V~~A~~~I~~~L~e 200 (596)
..+-+|+ .+-|.||||.|.||+.++.-||+.|.|.. +..+|.|+| ++---+.|...+...+.+
T Consensus 212 ~~v~lp~d~mkgriigreGrnir~~e~~tgvd~iidd-------tp~~v~ls~~~~~rre~a~~~l~~l~~d 276 (520)
T PRK12704 212 SVVNLPNDEMKGRIIGREGRNIRALETLTGVDLIIDD-------TPEAVILSGFDPIRREIARLALEKLVQD 276 (520)
T ss_pred eeeecCCchhhcceeCCCcchHHHHHHHhCCeEEEcC-------CCCeEEEecCChhhHHHHHHHHHHHHhc
Confidence 3445565 88999999999999999999999999976 456788998 455544666666666654
No 94
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=92.74 E-value=0.48 Score=52.41 Aligned_cols=92 Identities=17% Similarity=0.232 Sum_probs=66.6
Q ss_pred HHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEE
Q 007603 101 TQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQI 180 (596)
Q Consensus 101 A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I 180 (596)
|.+|-..|++.+..+-...-.......++...|-|+.+....+||.+|...|+|..|||+.-++ ++..+.|
T Consensus 569 a~~ar~~Il~~m~k~i~~Pr~~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v---------De~t~~i 639 (760)
T KOG1067|consen 569 AREARLQILDIMEKNINSPRGSDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV---------DEGTFSI 639 (760)
T ss_pred hhHHHHHHHHHHHhhcCCcccCccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee---------cCceEEE
Confidence 3344444554443332222122233457888899999999999999999999999999966555 4567777
Q ss_pred eec-HHHHHHHHHHHHHHHhcc
Q 007603 181 TGA-TLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 181 ~G~-~e~V~~A~~~I~~~L~e~ 201 (596)
-.. ..+.++|...|..++...
T Consensus 640 ~A~~~~am~~Ak~~I~~i~~~~ 661 (760)
T KOG1067|consen 640 FAPTQAAMEEAKEFIDGIIKDD 661 (760)
T ss_pred EecCHHHHHHHHHHHHHHhcCc
Confidence 765 889999999999998763
No 95
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=92.69 E-value=1.3 Score=43.71 Aligned_cols=127 Identities=14% Similarity=0.099 Sum_probs=85.0
Q ss_pred EEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCC
Q 007603 277 RMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGF 356 (596)
Q Consensus 277 ~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~ 356 (596)
.+.++....-.+...+|..++.|....|++|.+... +..+.|+|++ + +.+.+......+.
T Consensus 29 ~v~l~~~~~~LLl~~~~~~L~~l~~~~~~~I~~~~~-----~~~i~I~g~k------~-~~~~i~~~i~~~l-------- 88 (210)
T PF14611_consen 29 DVWLQPDEFFLLLTGNGRILENLAARNGAKIEVSRS-----ENRIRITGTK------S-TAEYIEASINEIL-------- 88 (210)
T ss_pred EEEecchheeeeecCCchHHHHHHHhcCceEEEecC-----CcEEEEEccH------H-HHHHHHHHHHHHH--------
Confidence 344557777888999999999998888999999843 4579999984 2 2233332222222
Q ss_pred CCCCCCCCceEEEEEeccccccccccC----CCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEc-----CCHHHH
Q 007603 357 SSGENKGDAVAVSILVGADFVGCLTGS----GSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQIS-----GEYKNV 427 (596)
Q Consensus 357 ~~g~~~~~~~t~~l~VP~~~vG~IIGk----gG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~-----G~~~~V 427 (596)
....+.++.++.-.--.--++ ....+++|++.|++.|+..+.+ ..+.|+ -....+
T Consensus 89 ------~~i~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie~~~~~----------~~~~i~~~~~~~~~~~~ 152 (210)
T PF14611_consen 89 ------SNIRTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIEKNPDG----------NKLKISWLASPENEKRA 152 (210)
T ss_pred ------hhcEEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEEECCCC----------CeEEEEEEeeccccchH
Confidence 123466777664322111111 4678999999999999886532 234444 456789
Q ss_pred HHHHHHHHHHHh
Q 007603 428 QNALSEVVGRLR 439 (596)
Q Consensus 428 ~~A~~~I~~~Lr 439 (596)
+.|++++...+.
T Consensus 153 ~~a~RlL~~a~~ 164 (210)
T PF14611_consen 153 DRAKRLLLWALD 164 (210)
T ss_pred HHHHHHHHHhcc
Confidence 999999988774
No 96
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=90.21 E-value=0.15 Score=41.56 Aligned_cols=35 Identities=17% Similarity=0.273 Sum_probs=29.8
Q ss_pred CCcEEEEEEeccCccceeecCCChHHHHHHHHhCc
Q 007603 22 DDVVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (596)
Q Consensus 22 ~~~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga 56 (596)
.+...+.+-|..+..|.||||+|.+++.||.-.+.
T Consensus 26 ~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~ 60 (73)
T PF13083_consen 26 EDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNA 60 (73)
T ss_dssp TTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHH
T ss_pred CCceEEEEEECCCccceEECCCCeeHHHHHHHHHH
Confidence 45567778889999999999999999999987654
No 97
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=90.07 E-value=0.2 Score=59.24 Aligned_cols=71 Identities=17% Similarity=-0.032 Sum_probs=59.9
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (596)
...++.+|-....+|||++|.+|+.++..|||.|.|.+-.. ....||.+.+.|.++.++.|...|.--+.+
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~----~Nqaers~~~kg~p~~~r~a~~~I~~~i~D 1410 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQP----DNQAERSKAPKGRPPSQRVATSPIGLPIID 1410 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCC----ccchhhhcccCCCChhhhhhhccccceeec
Confidence 45677889989999999999999999999999999987222 135689999999999999999988765554
No 98
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=89.49 E-value=0.59 Score=36.61 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=28.0
Q ss_pred cEEEEEEeccCccceeecCCChHHHHHHHHhCceE
Q 007603 24 VVSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (596)
Q Consensus 24 ~~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I 58 (596)
.....+.+.....|.+||++|.+++.|+..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35555666666789999999999999999998544
No 99
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=89.26 E-value=0.23 Score=58.74 Aligned_cols=63 Identities=19% Similarity=0.056 Sum_probs=52.4
Q ss_pred EEEEEEeccCccceeecCCChHHHHHHHHhCceEEEeC-CCCCCCceEEEEccCcchhhhhhhc
Q 007603 25 VSFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG-GFPGSDHRVILVVGSGSIDRRIMFC 87 (596)
Q Consensus 25 ~~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~-~~~g~~eRvi~I~G~~e~~~~a~~~ 87 (596)
...++-+|-..+.+|||++|+||+.+|.-||+.|+|.. -..+..||-+++.|.++.++-+...
T Consensus 1340 ~~~k~~~P~~a~SRVig~ggsnVna~r~~tga~ielekmq~~Nqaers~~~kg~p~~~r~a~~~ 1403 (2131)
T KOG4369|consen 1340 NQGKGDGPLYASSRVIGDGGSNVNAARLGTGALIELEKMQPDNQAERSKAPKGRPPSQRVATSP 1403 (2131)
T ss_pred cccccccchhhhhhhhccCcchhhhHhhccceEEehhhcCCccchhhhcccCCCChhhhhhhcc
Confidence 34567789999999999999999999999999999987 3344689999999999887655443
No 100
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.36 E-value=1.1 Score=49.63 Aligned_cols=91 Identities=13% Similarity=0.128 Sum_probs=65.2
Q ss_pred HHHHHHHHHhhhhhccccCCCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCC
Q 007603 336 VQNAAVLVFARSVEVEGQQGFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQND 415 (596)
Q Consensus 336 a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~e 415 (596)
+.+|-..|++.|......+-. ...+...+..+|.|+.+....+||.+|...|+|..+||+--.+ ++
T Consensus 569 a~~ar~~Il~~m~k~i~~Pr~--~~~~y~P~~~tlkv~~sk~~~lIGp~G~~~kki~~EtGai~~v------------De 634 (760)
T KOG1067|consen 569 AREARLQILDIMEKNINSPRG--SDKEYSPVLETLKVSPSKRATLIGPGGVLKKKIEVETGAISQV------------DE 634 (760)
T ss_pred hhHHHHHHHHHHHhhcCCccc--CccccCceeeEEeecchhhheeecCccceeeeEeeeccceeee------------cC
Confidence 345556677777543221111 1123567899999999999999999999999999999954444 24
Q ss_pred cEEEEcC-CHHHHHHHHHHHHHHHhh
Q 007603 416 VVIQISG-EYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 416 r~V~I~G-~~~~V~~A~~~I~~~Lr~ 440 (596)
.+++|.- ++...++|+.+|.+.+.+
T Consensus 635 ~t~~i~A~~~~am~~Ak~~I~~i~~~ 660 (760)
T KOG1067|consen 635 GTFSIFAPTQAAMEEAKEFIDGIIKD 660 (760)
T ss_pred ceEEEEecCHHHHHHHHHHHHHHhcC
Confidence 5566655 467889999999887765
No 101
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=86.88 E-value=0.36 Score=46.55 Aligned_cols=54 Identities=28% Similarity=0.417 Sum_probs=48.0
Q ss_pred cccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHh
Q 007603 374 ADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLR 439 (596)
Q Consensus 374 ~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr 439 (596)
+..+|+|+||+|.+---|.+.|..+|.+.+ ..|.|-|..++++.|...|+..|-
T Consensus 177 sRAIGRiaGk~GkTkfaIEn~trtrIVlad------------~kIHiLG~~~niriAR~avcsLIl 230 (252)
T KOG3273|consen 177 SRAIGRIAGKGGKTKFAIENVTRTRIVLAD------------SKIHILGAFQNIRIARDAVCSLIL 230 (252)
T ss_pred HHHHHHhhcCCCcceeeeeccceeEEEecC------------ceEEEeecchhhHHHHHhhHhhhc
Confidence 468999999999999999999999998863 569999999999999999987543
No 102
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.77 E-value=0.69 Score=37.48 Aligned_cols=39 Identities=21% Similarity=0.291 Sum_probs=31.0
Q ss_pred EEEEEecccc-----ccccccCCCchhHHHHHHh-CCeEEEeCCC
Q 007603 367 AVSILVGADF-----VGCLTGSGSSAVSEMEDVT-GTDIKLVGGE 405 (596)
Q Consensus 367 t~~l~VP~~~-----vG~IIGkgG~~Ik~I~~~T-Ga~I~I~~~~ 405 (596)
...+.|-+.. +|..||++|+.|+.|.++. |-+|+|-.-+
T Consensus 4 r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~~s 48 (69)
T PF13184_consen 4 RTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVEYS 48 (69)
T ss_dssp EEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE--
T ss_pred eEEEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEEcC
Confidence 5667777777 9999999999999999999 9999997643
No 103
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=86.47 E-value=0.55 Score=38.05 Aligned_cols=35 Identities=26% Similarity=0.391 Sum_probs=27.4
Q ss_pred EEEeccCc-----cceeecCCChHHHHHHHHh-CceEEEeC
Q 007603 28 RLVCPTPV-----VGGLIGRSGSIISSIRRDT-KCRIHCEG 62 (596)
Q Consensus 28 rilvP~~~-----vg~IIGk~G~~Ik~Ir~eT-ga~I~V~~ 62 (596)
.+.|-+.. +|..||++|+.|+.|.++. |-+|+|=.
T Consensus 6 kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~gekIdvV~ 46 (69)
T PF13184_consen 6 KVAVKSGDPNIDPVGACIGKKGSRIKAISEELNGEKIDVVE 46 (69)
T ss_dssp EEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTTT-EEEEEE
T ss_pred EEEEEcCCCCcCcceecCccccHHHHHHHHHhCCCeEEEEE
Confidence 45556666 9999999999999999999 88888743
No 104
>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=85.94 E-value=1.2 Score=34.83 Aligned_cols=35 Identities=11% Similarity=0.260 Sum_probs=29.0
Q ss_pred ceEEEEEeccccccccccCCCchhHHHHHHhCCeE
Q 007603 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI 399 (596)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I 399 (596)
.....+.+.....|.+||++|++|+.++..++-.+
T Consensus 24 ~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 24 RIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred cEEEEEEECCCCCceEECCCCccHHHHHHHHHHHc
Confidence 35666777776789999999999999999998554
No 105
>KOG3273 consensus Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=85.86 E-value=0.69 Score=44.70 Aligned_cols=57 Identities=26% Similarity=0.332 Sum_probs=50.9
Q ss_pred ccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhcc
Q 007603 136 NTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQHL 201 (596)
Q Consensus 136 p~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e~ 201 (596)
-+..+|.|+||+|.+--.|++-|-++|.+.. ..|.|-|..++++-|...|+.++...
T Consensus 176 lsRAIGRiaGk~GkTkfaIEn~trtrIVlad---------~kIHiLG~~~niriAR~avcsLIlGs 232 (252)
T KOG3273|consen 176 LSRAIGRIAGKGGKTKFAIENVTRTRIVLAD---------SKIHILGAFQNIRIARDAVCSLILGS 232 (252)
T ss_pred HHHHHHHhhcCCCcceeeeeccceeEEEecC---------ceEEEeecchhhHHHHHhhHhhhccC
Confidence 3457899999999999999999999999943 56999999999999999999999764
No 106
>PRK12705 hypothetical protein; Provisional
Probab=84.54 E-value=1.3 Score=49.52 Aligned_cols=62 Identities=15% Similarity=0.262 Sum_probs=44.1
Q ss_pred EEEecc-ceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeec-HHHHHHHHHHHHHHHhc
Q 007603 132 GLLANT-TKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGA-TLAVKKALVAVTTCLQH 200 (596)
Q Consensus 132 rllVp~-~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~-~e~V~~A~~~I~~~L~e 200 (596)
.+-+|+ .+-|.||||.|.+|+.++..||+.+.|.. +.+.|.|++- +.--+.|...+..++.+
T Consensus 201 ~v~lp~demkGriIGreGrNir~~E~~tGvdliidd-------tp~~V~ls~fdp~rreia~~~l~~Li~d 264 (508)
T PRK12705 201 VVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD-------TPEAVVISSFNPIRREIARLTLEKLLAD 264 (508)
T ss_pred eeecCChHhhccccCccchhHHHHHHhhCCceEecC-------CccchhhcccCccchHHHHHHHHHHHhc
Confidence 344454 78999999999999999999999999976 3344666664 44444455555555543
No 107
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=84.38 E-value=0.48 Score=38.55 Aligned_cols=36 Identities=11% Similarity=0.255 Sum_probs=30.2
Q ss_pred CceEEEEEeccccccccccCCCchhHHHHHHhCCeE
Q 007603 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDI 399 (596)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I 399 (596)
......+.+..+..|.||||+|.+++.||.-.++-+
T Consensus 27 ~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~ 62 (73)
T PF13083_consen 27 DGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAA 62 (73)
T ss_dssp TTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHH
T ss_pred CceEEEEEECCCccceEECCCCeeHHHHHHHHHHHH
Confidence 445888889999999999999999999997665443
No 108
>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=81.96 E-value=0.82 Score=37.61 Aligned_cols=33 Identities=27% Similarity=0.428 Sum_probs=28.5
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCceEE
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH 59 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~ 59 (596)
..+.+...+.|.|||++|++|++|+++.+-.+.
T Consensus 27 ~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~ 59 (78)
T PF07650_consen 27 IIIVIKASQPGIVIGKKGSNIKKIREELRKELE 59 (78)
T ss_dssp EEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHH
T ss_pred EEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHh
Confidence 457788999999999999999999998876553
No 109
>PRK13764 ATPase; Provisional
Probab=80.56 E-value=1.8 Score=49.52 Aligned_cols=45 Identities=16% Similarity=0.209 Sum_probs=40.7
Q ss_pred CceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCccc
Q 007603 364 DAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVL 408 (596)
Q Consensus 364 ~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P 408 (596)
......+.||.+.++.+|||+|.+|++|.+..|.+|+|-..++.|
T Consensus 479 ~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~~~~~~ 523 (602)
T PRK13764 479 SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEP 523 (602)
T ss_pred cCCeEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEEccccc
Confidence 445888999999999999999999999999999999998877754
No 110
>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=80.50 E-value=1.1 Score=37.46 Aligned_cols=35 Identities=11% Similarity=0.217 Sum_probs=30.7
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCceEEEe
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE 61 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~ 61 (596)
.++.+....-|.|||++|++|++|+++..-...+.
T Consensus 32 i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~ 66 (81)
T cd02413 32 TEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFP 66 (81)
T ss_pred EEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCC
Confidence 77888999999999999999999999987666653
No 111
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=80.23 E-value=1.9 Score=43.75 Aligned_cols=51 Identities=14% Similarity=0.331 Sum_probs=46.5
Q ss_pred eeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHHHHHHHHHHHHHHhc
Q 007603 141 GVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLAVKKALVAVTTCLQH 200 (596)
Q Consensus 141 G~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~V~~A~~~I~~~L~e 200 (596)
-+|||.+|++++.|+--|.|.|-|.. .+|.+.|....+..+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG---------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG---------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC---------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 46999999999999999999999965 4789999999999999999999976
No 112
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=80.16 E-value=1.8 Score=35.64 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=27.3
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCceEEE
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V 60 (596)
+.+-+..+..|.+|||+|+++..||--++.-++-
T Consensus 26 i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 26 VEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 4455567889999999999999999888765443
No 113
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=79.52 E-value=2 Score=40.97 Aligned_cols=32 Identities=19% Similarity=0.294 Sum_probs=27.8
Q ss_pred EEeccCccceeecCCChHHHHHHHHhCceEEEe
Q 007603 29 LVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCE 61 (596)
Q Consensus 29 ilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~ 61 (596)
++|-... |..|||+|++|++|++..|-+|.|=
T Consensus 65 fvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevV 96 (166)
T PRK06418 65 LLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVV 96 (166)
T ss_pred EEEeCCC-cccccccchHHHHHHHHhCCcEEEE
Confidence 4555556 9999999999999999999999984
No 114
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=78.58 E-value=1.7 Score=47.49 Aligned_cols=41 Identities=20% Similarity=0.306 Sum_probs=37.7
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCc
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~ 406 (596)
..+.+.||..+++.+|||+|.+|++|.+..|-+|.|...+.
T Consensus 486 ~~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~e~ 526 (604)
T COG1855 486 GRAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEE 526 (604)
T ss_pred CeEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEccc
Confidence 46789999999999999999999999999999999987655
No 115
>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=78.04 E-value=2.1 Score=35.20 Aligned_cols=35 Identities=14% Similarity=0.296 Sum_probs=29.0
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEE
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKL 401 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I 401 (596)
...+.|..+..|.||||.|++++.||--+..-+.-
T Consensus 25 ~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~ 59 (77)
T cd02414 25 TVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNR 59 (77)
T ss_pred EEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhh
Confidence 56677778899999999999999999887765543
No 116
>PRK12705 hypothetical protein; Provisional
Probab=77.05 E-value=3.7 Score=46.04 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=35.2
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHHhCCeEEEeC
Q 007603 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTGTDIKLVG 403 (596)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~ 403 (596)
..+...+.+|+ ++-|+|||+.|.+|+-+...||+.|.|.+
T Consensus 196 e~tvs~v~lp~demkGriIGreGrNir~~E~~tGvdliidd 236 (508)
T PRK12705 196 DLSVSVVPIPSDAMKGRIIGREGRNIRAFEGLTGVDLIIDD 236 (508)
T ss_pred hheeeeeecCChHhhccccCccchhHHHHHHhhCCceEecC
Confidence 34566777887 79999999999999999999999999975
No 117
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=75.83 E-value=1.8 Score=47.18 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=34.1
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCceEEEeCC
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEGG 63 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~~ 63 (596)
...+.||.+..+.+|||+|.+|++|++..|-+|+|...
T Consensus 487 ~avv~vpe~~i~~vigk~g~~i~~ie~klgi~I~v~~~ 524 (604)
T COG1855 487 RAVVKVPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPL 524 (604)
T ss_pred eEEEEeCHHHhhHHhhcccchHHHHHHHhCCceEEEEc
Confidence 35577899999999999999999999999999999653
No 118
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=74.93 E-value=5.5 Score=40.60 Aligned_cols=51 Identities=20% Similarity=0.290 Sum_probs=45.7
Q ss_pred cccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhh
Q 007603 378 GCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRH 440 (596)
Q Consensus 378 G~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~ 440 (596)
-+|||.+|++++.|+-.|.|-|-|.. .+|.+.|....++.+...+.+++..
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG------------~TVsaiGpfkGlkevr~IV~DcM~N 211 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQG------------NTVSAIGPFKGLKEVRKIVEDCMKN 211 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeC------------cEEEeecCcchHHHHHHHHHHHHhc
Confidence 37999999999999999999998863 6799999999999999999887764
No 119
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=74.58 E-value=6.3 Score=39.57 Aligned_cols=48 Identities=19% Similarity=0.236 Sum_probs=41.1
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHH
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK 425 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~ 425 (596)
-.-+.|++..|.++||++|+.++-+.+.|+|+|-|-. +-.|=|.|..+
T Consensus 147 G~iv~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~-----------NG~IWV~~~~~ 194 (239)
T COG1097 147 GQIVKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQ-----------NGRIWVDGENE 194 (239)
T ss_pred CEEEEEchhhcceEecCCCcHHHHhhhhcCeEEEEec-----------CCEEEecCCCc
Confidence 4568899999999999999999999999999998864 45577777766
No 120
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=74.55 E-value=5.5 Score=40.00 Aligned_cols=57 Identities=19% Similarity=0.298 Sum_probs=43.7
Q ss_pred EEeccceeeeeeecCchhhhhhccccccEEEecCCCCCCCCCCcEEEEeecHHH-HHHHHHHHHHH
Q 007603 133 LLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPPACAAIDDQLIQITGATLA-VKKALVAVTTC 197 (596)
Q Consensus 133 llVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p~~~~~~dRiV~I~G~~e~-V~~A~~~I~~~ 197 (596)
+.|+...+..+|||+|+.++.+.++++|+|.|-.+ ..|-|.|..+. ..-|...|..+
T Consensus 150 v~i~p~kVpRvig~~~sm~~~l~~~~~~~I~VG~N--------G~IWV~~~~~~~e~~~~~aI~~i 207 (239)
T COG1097 150 VKIPPSKVPRVIGKKGSMLNMLKEKTGCEIIVGQN--------GRIWVDGENESLEELAIEAIRKI 207 (239)
T ss_pred EEEchhhcceEecCCCcHHHHhhhhcCeEEEEecC--------CEEEecCCCcchHHHHHHHHHHH
Confidence 66899999999999999999999999999999763 34667776553 44444444433
No 121
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=74.35 E-value=4.3 Score=37.68 Aligned_cols=38 Identities=24% Similarity=0.415 Sum_probs=33.3
Q ss_pred EEEEEeccceeeeeeecCchhhhhhccccccEEEecCC
Q 007603 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPP 167 (596)
Q Consensus 130 t~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~ 167 (596)
+-.+.|-...-|.+|||+|.++++|..+||=.-.|.+.
T Consensus 77 tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRt 114 (145)
T cd02410 77 TGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRT 114 (145)
T ss_pred CcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEec
Confidence 34577778888999999999999999999999888775
No 122
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=74.19 E-value=1.5 Score=36.08 Aligned_cols=35 Identities=14% Similarity=0.304 Sum_probs=29.8
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEE
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIK 400 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~ 400 (596)
....+.+-..+-|.|||++|++|++|.+..+-.++
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 46788889999999999999999999887766553
No 123
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=73.37 E-value=13 Score=41.19 Aligned_cols=103 Identities=12% Similarity=0.123 Sum_probs=71.4
Q ss_pred EEEEEeccccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccC
Q 007603 275 ALRMLFSGWTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQ 354 (596)
Q Consensus 275 ~~~l~VP~~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~ 354 (596)
.+.+.||..+|..|||.||..|+++..+.++.|++..... + |. .+ -++
T Consensus 450 e~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~----~-----~q-----------s~---~~d--------- 497 (657)
T COG5166 450 EIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYK----F-----GQ-----------SQ---WHD--------- 497 (657)
T ss_pred heEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhh----c-----ch-----------hh---hhc---------
Confidence 3457799999999999999999999998888887763210 0 00 00 000
Q ss_pred CCCCCCCCCCceEEEEEeccccccccccCCCchhHHHHHHh----CCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHH
Q 007603 355 GFSSGENKGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVT----GTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNA 430 (596)
Q Consensus 355 g~~~g~~~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~T----Ga~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A 430 (596)
..-+.-|.+..+.|+|++......+++.. ...|++.+ ..-++.++-|-...+...
T Consensus 498 ------------NV~I~~PrKn~~ni~~~KNd~~~~V~~~c~f~~Kgdirf~~---------~~~sI~~v~~~~~~I~rv 556 (657)
T COG5166 498 ------------NVLIEAPRKNQDNISGKKNDKLDKVKQQCRFNLKGDIRFCP---------QSTSIFTVDIYSDEIERV 556 (657)
T ss_pred ------------ceEEECCccCccchhcccccHHHHHhhhcccccccceEEcC---------CceEEEEEcccccHHHHH
Confidence 23456688899999999999888888766 55677754 223477777766655443
No 124
>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=72.04 E-value=3.6 Score=36.36 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=27.0
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCce
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~ 57 (596)
++|.+....-|.|||++|++|++|+++....
T Consensus 63 i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~ 93 (109)
T cd02412 63 VEVTIHTARPGIIIGKKGAGIEKLRKELQKL 93 (109)
T ss_pred EEEEEEeCCCCcccCCchHHHHHHHHHHHHH
Confidence 6778888999999999999999999887543
No 125
>PRK13764 ATPase; Provisional
Probab=71.41 E-value=3.4 Score=47.38 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=33.6
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCceEEEeC
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG 62 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~ 62 (596)
...+.||.+.++.+|||+|.+|++|++..|.+|+|..
T Consensus 482 ~~~v~~~~~~~~~~~~k~~~~~~~~~~~~~~~i~v~~ 518 (602)
T PRK13764 482 KAVVYVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRP 518 (602)
T ss_pred eEEEEEChhhhhHHhccCcchHHHHHHHhCCceEEEE
Confidence 4457789999999999999999999999999999964
No 126
>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=69.36 E-value=5.1 Score=33.68 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=24.8
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhC
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTK 55 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTg 55 (596)
+++.+....-|.+||++|.+|++|++...
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~l~ 68 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEILE 68 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHHHH
Confidence 56666778999999999999999998763
No 127
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=67.75 E-value=11 Score=41.69 Aligned_cols=97 Identities=24% Similarity=0.327 Sum_probs=60.4
Q ss_pred eeecCCChHHHHHHHHhCceEEEeCCCCCCCceEEEEccCcchhhhhhhccccccccCCCccHHHHHHHHHHHHHHhhhh
Q 007603 38 GLIGRSGSIISSIRRDTKCRIHCEGGFPGSDHRVILVVGSGSIDRRIMFCENDVVVEGGEVSSTQEAVIRVFERMWEVEA 117 (596)
Q Consensus 38 ~IIGk~G~~Ik~Ir~eTga~I~V~~~~~g~~eRvi~I~G~~e~~~~a~~~~~~~~~e~~~~~~A~~Al~~i~~~i~~~~~ 117 (596)
.+|-+.|.-|++|.++..-+|.|..... ...+..+|...|.+-+-+ +.
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dPs-------------------------------vl~~~e~A~~~I~eivP~-ea 89 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDPS-------------------------------VLKPPEEARKIILEIVPE-EA 89 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCch-------------------------------hcCCHHHHHHHHHHhCcc-cc
Confidence 4566778888888888887777743210 022233444444433322 11
Q ss_pred ccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhhccccccEEEecCCC
Q 007603 118 EVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP 168 (596)
Q Consensus 118 ~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p 168 (596)
+-.+ -.=...+-.++|-...-|.+|||+|++.++|..++|-.-.|.+.|
T Consensus 90 ~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~P 138 (637)
T COG1782 90 GITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTP 138 (637)
T ss_pred Ccee--EEecCCCceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecC
Confidence 1000 000022455888889999999999999999999999888887753
No 128
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=66.20 E-value=5.1 Score=40.05 Aligned_cols=31 Identities=26% Similarity=0.402 Sum_probs=27.0
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCc
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga 56 (596)
..+|.+....-|.|||++|++|++|+++...
T Consensus 52 ~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k 82 (233)
T COG0092 52 GTRVTIHAARPGLVIGKKGSNIEKLRKELEK 82 (233)
T ss_pred ceEEEEEeCCCcceEcCCCccHHHHHHHHHH
Confidence 4678889999999999999999999887643
No 129
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=63.13 E-value=9.6 Score=36.33 Aligned_cols=38 Identities=18% Similarity=0.249 Sum_probs=33.0
Q ss_pred eEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCC
Q 007603 366 VAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGG 404 (596)
Q Consensus 366 ~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~ 404 (596)
-..-+.|.+.. |.-|||+|++|+.+++..|-+|+|-.-
T Consensus 61 drvIfvV~~gd-g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 61 DLVILLVTSGP-RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred CEEEEEEeCCC-cccccccchHHHHHHHHhCCcEEEEEc
Confidence 36677777777 999999999999999999999999763
No 130
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=62.84 E-value=11 Score=41.71 Aligned_cols=98 Identities=19% Similarity=0.233 Sum_probs=67.5
Q ss_pred ccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhccccCCCCCCCCCCCce
Q 007603 287 GIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVEGQQGFSSGENKGDAV 366 (596)
Q Consensus 287 ~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~~~~g~~~g~~~~~~~ 366 (596)
.++-+.|..||+|.++..-+|.|-... ....+...|...|.+.+.+...-.. -.-...
T Consensus 42 ~~~~~~~dlik~lAk~lrKRI~iR~dP-----------------svl~~~e~A~~~I~eivP~ea~i~~-----i~Fd~~ 99 (637)
T COG1782 42 ELFAKDGDLIKDLAKDLRKRIIIRPDP-----------------SVLKPPEEARKIILEIVPEEAGITD-----IYFDDD 99 (637)
T ss_pred HHhccchhHHHHHHHHHhhceEeccCc-----------------hhcCCHHHHHHHHHHhCccccCcee-----EEecCC
Confidence 355578899999999988888776321 1123345676666666533210000 011334
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCc
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQ 406 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~ 406 (596)
+-++.|-.+.=|.+|||+|++.++|.++||-.-+|.+...
T Consensus 100 tGEViIea~KPGlvigk~g~~~reI~~~tgW~p~ivR~PP 139 (637)
T COG1782 100 TGEVIIEAKKPGLVIGKGGSTLREITAETGWAPKIVRTPP 139 (637)
T ss_pred CceEEEEecCCceEEecCchHHHHHHHHhCCcceeeecCC
Confidence 6788888999999999999999999999999998887443
No 131
>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=60.86 E-value=6.1 Score=33.02 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=28.5
Q ss_pred EEEEEeccceeeeeeecCchhhhhhccccccEEEe
Q 007603 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVM 164 (596)
Q Consensus 130 t~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I 164 (596)
.+++.+....-|.|||++|+.|++|+++-.-...+
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 47788888889999999999999999876544444
No 132
>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=59.92 E-value=10 Score=35.25 Aligned_cols=96 Identities=19% Similarity=0.211 Sum_probs=63.3
Q ss_pred ccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhc-cccCCCCCCCCCCCceE
Q 007603 289 IGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEV-EGQQGFSSGENKGDAVA 367 (596)
Q Consensus 289 IGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~-~~~~g~~~g~~~~~~~t 367 (596)
+-..|..|++|.++..-+|.|-.+. ....+-.+|...|.+.+-+. .+.. -.-...+
T Consensus 21 ~~~~~dli~~lAk~lrKRIvvR~dp-----------------s~l~~~e~A~~~I~~ivP~ea~i~d------i~Fd~~t 77 (145)
T cd02410 21 FAEDGDLVKDLAKDLRKRIVIRPDP-----------------SVLKPPEEAIKIILEIVPEEAGITD------IYFDDDT 77 (145)
T ss_pred HhcccHHHHHHHHHHhceEEEcCCh-----------------hhcCCHHHHHHHHHHhCCCccCcee------eEecCCC
Confidence 3456788999988877777664221 01123345665665555321 0000 0113346
Q ss_pred EEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcc
Q 007603 368 VSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV 407 (596)
Q Consensus 368 ~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~ 407 (596)
-++.|-...-|.+||++|.++++|...||=.-+|.+...+
T Consensus 78 GEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpPi 117 (145)
T cd02410 78 GEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPPI 117 (145)
T ss_pred cEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCCC
Confidence 6888888999999999999999999999999999875443
No 133
>COG5166 Uncharacterized conserved protein [Function unknown]
Probab=53.20 E-value=12 Score=41.47 Aligned_cols=131 Identities=10% Similarity=0.079 Sum_probs=78.8
Q ss_pred ccccccccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchH-HHHHHHHHhhhhhccccCCCCCCCC
Q 007603 283 WTASGIIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPV-QNAAVLVFARSVEVEGQQGFSSGEN 361 (596)
Q Consensus 283 ~~vg~IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a-~~Av~~i~~~i~e~~~~~g~~~g~~ 361 (596)
+.-..+-||+.-++.+|.+..-|.+++.-... .+. .+.--|.. ..++ +++. +.+ ...
T Consensus 389 d~EdFl~gkkngK~TrIm~~v~c~~~~~i~~~-~gs-~~~~~~~g-----~~~~F~k~~----~~~-~~E---------- 446 (657)
T COG5166 389 DNEDFLRGKKNGKATRIMKGVSCSELSSIVSS-TGS-IVETNGIG-----EKMSFSKKL----SIP-PTE---------- 446 (657)
T ss_pred chHHHhccccCcchhhhhhhcccceeeEEEec-CCc-EEEEeccC-----cchhhHHHh----cCC-ccc----------
Confidence 33347888888889999999888755542111 112 23322321 0111 1111 111 111
Q ss_pred CCCceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHH---HHHHHHHHHHHHH
Q 007603 362 KGDAVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYK---NVQNALSEVVGRL 438 (596)
Q Consensus 362 ~~~~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~---~V~~A~~~I~~~L 438 (596)
=.-...+.+|...|..|||.||..|+++...-++.|++...-.+|.... ..-|.|.-+.. ++.-|+.-+.+++
T Consensus 447 --Fpae~~f~i~e~~h~~IIgtgG~~iQ~~m~kh~v~i~f~n~~~~~qs~~--~dNV~I~~PrKn~~ni~~~KNd~~~~V 522 (657)
T COG5166 447 --FPAEIAFIIMESGHEMIIGTGGIEIQENMVKHAVDIAFKNFYKFGQSQW--HDNVLIEAPRKNQDNISGKKNDKLDKV 522 (657)
T ss_pred --CchheEEEeecccceeeeccCchhhHHhhhhhhhhhhhhhhhhcchhhh--hcceEEECCccCccchhcccccHHHHH
Confidence 1126678899999999999999999999999999999988766665222 23355554443 3444555555555
Q ss_pred h
Q 007603 439 R 439 (596)
Q Consensus 439 r 439 (596)
.
T Consensus 523 ~ 523 (657)
T COG5166 523 K 523 (657)
T ss_pred h
Confidence 5
No 134
>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=50.05 E-value=17 Score=42.25 Aligned_cols=39 Identities=26% Similarity=0.487 Sum_probs=34.4
Q ss_pred EEEEEeccceeeeeeecCchhhhhhccccccEEEecCCC
Q 007603 130 YCGLLANTTKIGVVVGKGGRNVTRMRIESGAKIVMLPPP 168 (596)
Q Consensus 130 t~rllVp~~~vG~IIGKgG~~Ik~I~~esGa~I~I~~~p 168 (596)
+-.++|-...-|.+|||+|+++++|..+||-.-.|.+.|
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~ 132 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTP 132 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecC
Confidence 445788888899999999999999999999999998753
No 135
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=48.15 E-value=12 Score=31.42 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=22.3
Q ss_pred EEEEeccceeeeeeecCchhhhhhccc
Q 007603 131 CGLLANTTKIGVVVGKGGRNVTRMRIE 157 (596)
Q Consensus 131 ~rllVp~~~vG~IIGKgG~~Ik~I~~e 157 (596)
+++.+....-|.+||++|++|++|++.
T Consensus 40 i~V~I~t~~pg~iIGk~G~~I~~l~~~ 66 (85)
T cd02411 40 TQITIYAERPGMVIGRGGKNIRELTEI 66 (85)
T ss_pred EEEEEEECCCCceECCCchhHHHHHHH
Confidence 556666688899999999999998865
No 136
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=48.02 E-value=31 Score=39.98 Aligned_cols=97 Identities=20% Similarity=0.183 Sum_probs=65.3
Q ss_pred cccccchhhhhhhhccCeeEEEeCCCCCCCccEEEEEecCCCCCCCchHHHHHHHHHhhhhhcc-ccCCCCCCCCCCCce
Q 007603 288 IIGKRGAIVRSLQNASGALISFAAPLTKSGERVVTISALEYLDTRHSPVQNAAVLVFARSVEVE-GQQGFSSGENKGDAV 366 (596)
Q Consensus 288 IIGk~G~~Ik~I~~~tGa~I~i~~~~~~~~er~v~IsG~e~p~~~~~~a~~Av~~i~~~i~e~~-~~~g~~~g~~~~~~~ 366 (596)
.+-..|..||+|.++..-+|.|-.... ...+..+|...|.+.+.+.. +.. -.-...
T Consensus 37 ~~~~~~~~~~~~~~~~~~r~~~~~~~~-----------------~~~~~~~~~~~i~~~~~~~~~~~~------~~f~~~ 93 (630)
T TIGR03675 37 LFAKDDDLVKELAKKLRKRIVIRPDPS-----------------VLLPPEEAIEKIKEIVPEEAGITD------IYFDDV 93 (630)
T ss_pred HhccchHHHHHHHHHhhceEEEecChh-----------------hcCCHHHHHHHHHHhCCCcCCcee------EEecCC
Confidence 444678899999888887777652210 11233456655655553220 000 012345
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcc
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQV 407 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~ 407 (596)
+-++.|-...-|.+|||+|+++++|.++||-.-+|.+...+
T Consensus 94 ~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~~ 134 (630)
T TIGR03675 94 TGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPPI 134 (630)
T ss_pred CceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCCC
Confidence 67888999999999999999999999999999999875443
No 137
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=46.82 E-value=12 Score=37.62 Aligned_cols=30 Identities=27% Similarity=0.479 Sum_probs=25.8
Q ss_pred ceEEEEEeccceeeeeeecCchhhhhhccc
Q 007603 128 VAYCGLLANTTKIGVVVGKGGRNVTRMRIE 157 (596)
Q Consensus 128 ~vt~rllVp~~~vG~IIGKgG~~Ik~I~~e 157 (596)
...+++.|....-|.||||+|++|++|++.
T Consensus 50 ~~~~~V~I~aarPg~VIGk~G~~I~~L~~~ 79 (233)
T COG0092 50 PKGTRVTIHAARPGLVIGKKGSNIEKLRKE 79 (233)
T ss_pred CCceEEEEEeCCCcceEcCCCccHHHHHHH
Confidence 446788899999999999999999998754
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=46.36 E-value=17 Score=32.02 Aligned_cols=30 Identities=10% Similarity=0.236 Sum_probs=24.1
Q ss_pred EEEEEeccccccccccCCCchhHHHHHHhC
Q 007603 367 AVSILVGADFVGCLTGSGSSAVSEMEDVTG 396 (596)
Q Consensus 367 t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TG 396 (596)
..++.|-...-|.|||++|+.|++|++...
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 356666677789999999999999977644
No 139
>PF00936 BMC: BMC domain; InterPro: IPR000249 This domain is found in a variety of polyhedral organelle shell proteins, including CsoS1A, CsoS1B and CsoS1C of Thiobacillus neapolitanus (Halothiobacillus neapolitanus) and their orthologs from other bacteria. Some autotrophic and non-autotrophic organisms form polyhedral organelles, carboxysomes/enterosomes []. The best studied is the carboxysome of Halothiobacillus neapolitanus, which is composed of at least 9 proteins: six shell proteins, CsoS1A, CsoS1B, CsoS1C, Cso2A, Cso2B and CsoS3 (carbonic anhydrase) [], one protein of unknown function and the large and small subunits of RuBisCo (CbbL and Cbbs). Carboxysomes appear to be approximately 120 nm in diameter, most often observed as regular hexagons, with a solid interior bounded by a unilamellar protein shell. The interior is filled with type I RuBisCo, which is composed of 8 large subunits and 8 small subunits; it accounts for 60% of the carboxysomal protein, which amounts to approximately 300 molecules of enzyme per carboxysome. Carboxysomes are required for autotrophic growth at low CO2 concentrations and are thought to function as part of a CO2-concentrating mechanism [, ]. Polyhedral organelles, enterosomes, from non-autotrophic organisms are involved in coenzyme B12-dependent 1,2-propanediol utilisation (e.g., in Salmonella enterica []) and ethanolamine utilisation (e.g., in Salmonella typhimurium []). Genes needed for enterosome formation are located in the 1,2-propanediol utilisation pdu [, ] or ethanolamine utilisation eut [, ] operons, respectively. Although enterosomes of non-autotrophic organisms are apparently related to carboxysomes structurally, a functional relationship is uncertain. A role in CO2 concentration, similar to that of the carboxysome, is unlikely since there is no known association between CO2 and coenzyme B12-dependent 1,2-propanediol or ethanolamine utilisation []. It seems probable that entrosomes help protect the cells from reactive aldehyde species in the degradation pathways of 1,2-propanediol and ethanolamine [].; PDB: 3F56_C 3FCH_A 3I87_A 3GFH_B 3I82_A 3MPV_A 3IO0_A 4AXJ_B 3N79_A 2G13_A ....
Probab=41.32 E-value=29 Score=28.43 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=31.2
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHhhccccccccC
Q 007603 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILN 449 (596)
Q Consensus 414 ~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~ 449 (596)
..-.+.|+|+..+|+.|.+...+.+.+.++...+++
T Consensus 38 g~~~~~i~G~vs~V~~Av~a~~~~~~~~~v~~~vI~ 73 (75)
T PF00936_consen 38 GKVTVIITGDVSAVKAAVDAAEEAAGKKLVSSTVIP 73 (75)
T ss_dssp TEEEEEEEESHHHHHHHHHHHHHHHHHTEEEEEEES
T ss_pred CeEEEEEEECHHHHHHHHHHHHHHHhhceeeEEEeC
Confidence 367899999999999999999999998877776665
No 140
>cd07053 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=39.41 E-value=38 Score=27.95 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=32.0
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHhhccccccccCC
Q 007603 414 NDVVIQISGEYKNVQNALSEVVGRLRHNLKSGEILNE 450 (596)
Q Consensus 414 ~er~V~I~G~~~~V~~A~~~I~~~Lr~~~~~~~~~~~ 450 (596)
..-.+.|+|...+|+.|.+.-.+...+.+++..+++.
T Consensus 37 Gk~~vii~GdvsaV~~Av~a~~~~~~~~~v~~~vI~~ 73 (76)
T cd07053 37 GKYIIIVSGDVGAVQAAVDAGKEIGGKYVVDSFVLPN 73 (76)
T ss_pred CEEEEEEEEcHHHHHHHHHHHHHHhCCcEEEEEEeCC
Confidence 3557999999999999999999999988888878763
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=38.78 E-value=35 Score=34.89 Aligned_cols=30 Identities=20% Similarity=0.285 Sum_probs=24.2
Q ss_pred EEEEEEecc-CccceeecCCChHHHHHHHHh
Q 007603 25 VSFRLVCPT-PVVGGLIGRSGSIISSIRRDT 54 (596)
Q Consensus 25 ~~~rilvP~-~~vg~IIGk~G~~Ik~Ir~eT 54 (596)
+...|+|.. ++-+.|||++|+.||+|..+.
T Consensus 221 i~~~i~v~~~s~k~iiig~~g~~ik~i~~~a 251 (270)
T TIGR00436 221 IHALISVERESQKKIIIGKNGSMIKAIGIAA 251 (270)
T ss_pred EEEEEEECcCCceeEEEcCCcHHHHHHHHHH
Confidence 556677875 677899999999999987664
No 142
>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=38.46 E-value=31 Score=33.80 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=27.0
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCce
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~ 57 (596)
.+|.+....-|.|||++|.+|++|+++..-.
T Consensus 40 ~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~ 70 (195)
T TIGR01008 40 TKVIIFAERPGLVIGRGGRRIRELTEKLQKK 70 (195)
T ss_pred EEEEEEECCCceEECCCchHHHHHHHHHHHH
Confidence 6788888999999999999999999887543
No 143
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=37.98 E-value=31 Score=34.12 Aligned_cols=32 Identities=22% Similarity=0.271 Sum_probs=26.7
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCceE
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRI 58 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I 58 (596)
.++.+....-|.+||++|.+|++|++...-..
T Consensus 42 i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~ 73 (207)
T PRK04191 42 TRITIYAERPGMVIGRGGKNIRELTEILEKKF 73 (207)
T ss_pred EEEEEEECCCCeEECCCchhHHHHHHHHHHHh
Confidence 56666778899999999999999999876543
No 144
>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=37.96 E-value=31 Score=35.26 Aligned_cols=32 Identities=13% Similarity=0.104 Sum_probs=25.4
Q ss_pred ceEEEEEecc-ccccccccCCCchhHHHHHHhC
Q 007603 365 AVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTG 396 (596)
Q Consensus 365 ~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TG 396 (596)
.+.+.+.|.. ++-+-|||++|+.||+|.....
T Consensus 220 ~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar 252 (270)
T TIGR00436 220 KIHALISVERESQKKIIIGKNGSMIKAIGIAAR 252 (270)
T ss_pred EEEEEEEECcCCceeEEEcCCcHHHHHHHHHHH
Confidence 3677788875 6789999999999999865543
No 145
>CHL00048 rps3 ribosomal protein S3
Probab=37.11 E-value=33 Score=34.16 Aligned_cols=32 Identities=19% Similarity=0.158 Sum_probs=26.8
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCce
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCR 57 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~ 57 (596)
..+|.+....-|.|||++|.+|++|++...-.
T Consensus 67 ~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k~ 98 (214)
T CHL00048 67 LIQVIIYTGFPKLLIERKGRGIEELQINLQKE 98 (214)
T ss_pred eEEEEEEECCCceEECCCcHhHHHHHHHHHHH
Confidence 46677788889999999999999999887433
No 146
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=35.87 E-value=35 Score=34.15 Aligned_cols=33 Identities=12% Similarity=0.185 Sum_probs=27.8
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCceEE
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIH 59 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~ 59 (596)
.++.+....-|.|||++|..|++|+++..-.+.
T Consensus 46 i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~ 78 (220)
T PTZ00084 46 TEIIIRATRTREVLGDKGRRIRELTSLLQKRFG 78 (220)
T ss_pred EEEEEEECCCccEEcCCchHHHHHHHHHHHHhC
Confidence 677788888999999999999999988765443
No 147
>COG1159 Era GTPase [General function prediction only]
Probab=34.57 E-value=21 Score=37.12 Aligned_cols=33 Identities=12% Similarity=0.235 Sum_probs=25.8
Q ss_pred CceEEEEEecc-ccccccccCCCchhHHHHHHhC
Q 007603 364 DAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTG 396 (596)
Q Consensus 364 ~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TG 396 (596)
-.+...+.|+. ++-|-||||+|++||+|-..+.
T Consensus 227 ~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR 260 (298)
T COG1159 227 LKIHATIYVERESQKGIIIGKNGAMIKKIGTAAR 260 (298)
T ss_pred EEEEEEEEEecCCccceEECCCcHHHHHHHHHHH
Confidence 34677788876 7889999999999998865443
No 148
>PRK03818 putative transporter; Validated
Probab=33.89 E-value=2.3e+02 Score=32.35 Aligned_cols=131 Identities=15% Similarity=0.203 Sum_probs=69.2
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCceEEEeC---------CCCC---CCceEEEEccCcchhhhhhhccccccc
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHCEG---------GFPG---SDHRVILVVGSGSIDRRIMFCENDVVV 93 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V~~---------~~~g---~~eRvi~I~G~~e~~~~a~~~~~~~~~ 93 (596)
..++.|+++. ++ |++++++.......+.|.. +.++ ...+++.|.|..+..+++....+.+
T Consensus 206 ~r~~~V~~s~---li---GkTv~el~~~~~~~v~V~~I~R~g~~~~p~~~~~L~~GDiLlV~G~~e~l~~l~~~~Gl~-- 277 (552)
T PRK03818 206 TINIRVENPN---LH---GKAIKDVPILNGDKFVCSRLKRGDTLMVPSPDTIIQLGDLLHLVGQPEDLHKAQLVIGEE-- 277 (552)
T ss_pred eEEEEEeCCC---CC---CCcHHHHHhhhCCCEEEEEEEECCEEECCCCCCccCCCCEEEEEECHHHHHHHHHhcCCc--
Confidence 3556666443 34 6789999998877666531 1111 2345677777766543332222111
Q ss_pred cCCCccHHHHHHHHHHHHHHhhhhccCCCCCCCCceEEEEEeccceeeeeeecCchhhhhh--ccccccEEEecCC----
Q 007603 94 EGGEVSSTQEAVIRVFERMWEVEAEVEGDGDGDDVAYCGLLANTTKIGVVVGKGGRNVTRM--RIESGAKIVMLPP---- 167 (596)
Q Consensus 94 e~~~~~~A~~Al~~i~~~i~~~~~~~~~~~~~~~~vt~rllVp~~~vG~IIGKgG~~Ik~I--~~esGa~I~I~~~---- 167 (596)
. ..+.+...+.....++++|++ .++|| +++++ ++++|+.|.-..+
T Consensus 278 ----------------------~-~~~~~~~~~~~~~E~Vvv~~S---~liGk---TL~eL~~r~~~Gv~VlaI~R~g~~ 328 (552)
T PRK03818 278 ----------------------V-DTSLSTRGTDLRSERVVVTNE---KVLGK---KLRDLHLKNKYGVVISRLNRAGVE 328 (552)
T ss_pred ----------------------c-CccccccCcceEEEEEEEcCh---hccCC---cHHHhcccccCCeEEEEEeECCee
Confidence 0 000001112234445555654 55666 68877 4667777544433
Q ss_pred ----CCCCCCCCcEEEEeecHHHHHHHHHH
Q 007603 168 ----PACAAIDDQLIQITGATLAVKKALVA 193 (596)
Q Consensus 168 ----p~~~~~~dRiV~I~G~~e~V~~A~~~ 193 (596)
+...-..--++.+.|++++++++...
T Consensus 329 l~~~~d~~Lq~GD~LlVvG~~~~i~~l~~~ 358 (552)
T PRK03818 329 LVASPDLSLQFGDILNLVGRPEAIDAVANV 358 (552)
T ss_pred cCCCCCCEEecCCEEEEEECHHHHHHHHHH
Confidence 11111223457899999999987664
No 149
>PRK15494 era GTPase Era; Provisional
Probab=33.41 E-value=39 Score=35.94 Aligned_cols=30 Identities=17% Similarity=0.333 Sum_probs=24.3
Q ss_pred eEEEEEecc-ccccccccCCCchhHHHHHHh
Q 007603 366 VAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (596)
Q Consensus 366 ~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (596)
+...+.|.. ++-+-|||++|+.||+|....
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 667788876 688899999999999886543
No 150
>PRK00089 era GTPase Era; Reviewed
Probab=32.71 E-value=40 Score=34.66 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=23.9
Q ss_pred eEEEEEecc-ccccccccCCCchhHHHHHHh
Q 007603 366 VAVSILVGA-DFVGCLTGSGSSAVSEMEDVT 395 (596)
Q Consensus 366 ~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~T 395 (596)
+.+.+.|.. ++-+-|||++|++||+|....
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 667777865 677899999999999886543
No 151
>PRK15494 era GTPase Era; Provisional
Probab=31.54 E-value=51 Score=35.06 Aligned_cols=30 Identities=20% Similarity=0.324 Sum_probs=24.1
Q ss_pred EEEEEEecc-CccceeecCCChHHHHHHHHh
Q 007603 25 VSFRLVCPT-PVVGGLIGRSGSIISSIRRDT 54 (596)
Q Consensus 25 ~~~rilvP~-~~vg~IIGk~G~~Ik~Ir~eT 54 (596)
+...|+|.. ++-+.|||++|+.||+|..+.
T Consensus 273 i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~a 303 (339)
T PRK15494 273 INQVIVVSRESYKTIILGKNGSKIKEIGAKS 303 (339)
T ss_pred EEEEEEECCCCceeEEEcCCcHHHHHHHHHH
Confidence 456688876 578899999999999886654
No 152
>PRK00089 era GTPase Era; Reviewed
Probab=29.13 E-value=60 Score=33.38 Aligned_cols=30 Identities=17% Similarity=0.411 Sum_probs=23.2
Q ss_pred EEEEEEecc-CccceeecCCChHHHHHHHHh
Q 007603 25 VSFRLVCPT-PVVGGLIGRSGSIISSIRRDT 54 (596)
Q Consensus 25 ~~~rilvP~-~~vg~IIGk~G~~Ik~Ir~eT 54 (596)
+...|+|.. ++-+.|||++|+.||+|..+.
T Consensus 226 i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~a 256 (292)
T PRK00089 226 IEATIYVERDSQKGIIIGKGGAMLKKIGTEA 256 (292)
T ss_pred EEEEEEEccCCceeEEEeCCcHHHHHHHHHH
Confidence 455567765 567899999999999886654
No 153
>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=28.88 E-value=3.3e+02 Score=31.18 Aligned_cols=58 Identities=14% Similarity=0.237 Sum_probs=35.6
Q ss_pred EEEEEeccceeeeeeecCchhhhhhc------cccccEEEecCC--------CCCCCCCCcEEEEeecHHHHHHHHHH
Q 007603 130 YCGLLANTTKIGVVVGKGGRNVTRMR------IESGAKIVMLPP--------PACAAIDDQLIQITGATLAVKKALVA 193 (596)
Q Consensus 130 t~rllVp~~~vG~IIGKgG~~Ik~I~------~esGa~I~I~~~--------p~~~~~~dRiV~I~G~~e~V~~A~~~ 193 (596)
..++++|++ .++|| +++++. +.+|+.|.-..+ +...-..--++.+.|++++++++...
T Consensus 304 ~e~VV~~~S---~liGk---TL~eL~~r~~~~~~~Gv~Vl~I~R~g~~i~~~~d~~L~~GD~LlV~G~~~~l~~~~~~ 375 (562)
T TIGR03802 304 TKDVVLTNK---EYNGK---TVAEILKNAQQFMRHGVYVEKIKRDDQPLPILPETVLQRGDVVTLVGTPQDVDRAAKQ 375 (562)
T ss_pred EEEEEECCc---ccCCc---cHHHHhccccccccCCeEEEEEeeCCccccCCCCCEecCCCEEEEEeCHHHHHHHHHH
Confidence 444555554 45555 788886 267877655443 11111233457899999999987665
No 154
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=28.61 E-value=49 Score=34.81 Aligned_cols=34 Identities=15% Similarity=0.177 Sum_probs=27.5
Q ss_pred CCceEEEEEecc-ccccccccCCCchhHHHHHHhC
Q 007603 363 GDAVAVSILVGA-DFVGCLTGSGSSAVSEMEDVTG 396 (596)
Q Consensus 363 ~~~~t~~l~VP~-~~vG~IIGkgG~~Ik~I~~~TG 396 (596)
...+..++.+|. ++...||||||..|++|-++-+
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 346788899998 5677889999999999976654
No 155
>cd07045 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carbox
Probab=27.40 E-value=79 Score=26.55 Aligned_cols=36 Identities=19% Similarity=0.317 Sum_probs=30.2
Q ss_pred CcEEEEcCCHHHHHHHHHHHHHHHhh--ccccccccCC
Q 007603 415 DVVIQISGEYKNVQNALSEVVGRLRH--NLKSGEILNE 450 (596)
Q Consensus 415 er~V~I~G~~~~V~~A~~~I~~~Lr~--~~~~~~~~~~ 450 (596)
.-.+.|+|+..+|+.|.+...+..++ .++++.+++.
T Consensus 38 k~~vii~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~~ 75 (84)
T cd07045 38 LVTVKITGDVAAVKAAVEAGAAAAERIGELVSSHVIPR 75 (84)
T ss_pred EEEEEEEEcHHHHHHHHHHHHHHHhccCcEEEEEEeCC
Confidence 56899999999999999999988887 4777777753
No 156
>COG1159 Era GTPase [General function prediction only]
Probab=26.71 E-value=74 Score=33.22 Aligned_cols=30 Identities=20% Similarity=0.392 Sum_probs=23.0
Q ss_pred EEEEEEecc-CccceeecCCChHHHHHHHHh
Q 007603 25 VSFRLVCPT-PVVGGLIGRSGSIISSIRRDT 54 (596)
Q Consensus 25 ~~~rilvP~-~~vg~IIGk~G~~Ik~Ir~eT 54 (596)
+...|+|+. ++-+-||||+|+.||+|-.+.
T Consensus 229 I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~A 259 (298)
T COG1159 229 IHATIYVERESQKGIIIGKNGAMIKKIGTAA 259 (298)
T ss_pred EEEEEEEecCCccceEECCCcHHHHHHHHHH
Confidence 444577775 678899999999999876554
No 157
>cd07056 BMC_PduK 1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat 1l. PduK proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduK might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view.
Probab=26.21 E-value=80 Score=26.07 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=29.0
Q ss_pred CCcEEEEcCCHHHHHHHHHHHHHHHh--hccccccccC
Q 007603 414 NDVVIQISGEYKNVQNALSEVVGRLR--HNLKSGEILN 449 (596)
Q Consensus 414 ~er~V~I~G~~~~V~~A~~~I~~~Lr--~~~~~~~~~~ 449 (596)
..-.+.|+|+-.+|+.|.+...+..+ ..++++.+++
T Consensus 38 G~~~viv~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~ 75 (77)
T cd07056 38 GWMTVKISGDVAAVNAAIEAGKQTAGASDGYVASTVIA 75 (77)
T ss_pred eEEEEEEEeeHHHHHHHHHHHHHHHhccCCEEEEEEeC
Confidence 34668999999999999999998888 5566666664
No 158
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=25.90 E-value=55 Score=32.32 Aligned_cols=70 Identities=11% Similarity=0.218 Sum_probs=45.2
Q ss_pred ceEEEEEeccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhc
Q 007603 365 AVAVSILVGADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHN 441 (596)
Q Consensus 365 ~~t~~l~VP~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~ 441 (596)
.-+..+.+-.+..+.|||+.|++++.||-.+.+...-.. .....-+|-+-+=.+.-+..+..+..++.+.
T Consensus 90 ~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~-------g~~~~v~ldv~~yRerR~e~L~~LA~~~A~r 159 (208)
T COG1847 90 GRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIG-------GKFKRVTLDVGDYRERRKETLIKLAERAAER 159 (208)
T ss_pred CcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhc-------CcceEEEEEhhhHHHHHHHHHHHHHHHHHHH
Confidence 346778888888999999999999999998887774421 1112233444444444455555555555543
No 159
>KOG1423 consensus Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=25.81 E-value=63 Score=34.08 Aligned_cols=40 Identities=25% Similarity=0.380 Sum_probs=29.7
Q ss_pred CCCCCCC---cEEEEEEecc-CccceeecCCChHHHHHHHHhCc
Q 007603 17 PLNLPDD---VVSFRLVCPT-PVVGGLIGRSGSIISSIRRDTKC 56 (596)
Q Consensus 17 ~~~~~~~---~~~~rilvP~-~~vg~IIGk~G~~Ik~Ir~eTga 56 (596)
.|+..++ .+...++||. +....||||||..|++|-++.+-
T Consensus 317 ~w~e~~~g~l~I~~~v~~pK~s~~klliGkgG~ki~qI~~~a~~ 360 (379)
T KOG1423|consen 317 SWKERPAGVLFIQVEVVCPKNSQKKLLIGKGGKKISQIGTRANE 360 (379)
T ss_pred EeeecCCcEEEEEEEEEcCCCcceeEEEcCCCccHHHHHHHHHH
Confidence 4444444 4566799998 56678999999999999877654
No 160
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=25.32 E-value=1.4e+02 Score=31.78 Aligned_cols=51 Identities=20% Similarity=0.174 Sum_probs=43.5
Q ss_pred ccccccccccCCCchhHHHHHHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHH
Q 007603 373 GADFVGCLTGSGSSAVSEMEDVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVV 435 (596)
Q Consensus 373 P~~~vG~IIGkgG~~Ik~I~~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~ 435 (596)
+.+..-.|.|..+.+++.|.+.+|+.|... .+.++|+|+...|..|...+.
T Consensus 22 ~~~~~~~l~G~~~~~l~l~e~~~gv~i~~r------------G~~~~i~g~~~~v~~A~~~l~ 72 (348)
T COG1702 22 DDNELVALFGPTDTNLSLLEIALGVSIVAR------------GEAVRIIGARPLVDVATRVLL 72 (348)
T ss_pred CchhhhhhcCCCCccHHHHHHHhCcEEEeC------------CceEEEEechHHHHHHHHHHh
Confidence 356788899999999999999999999653 467999999878888887776
No 161
>cd07054 BMC_PduT_repeat2 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.
Probab=24.14 E-value=92 Score=25.80 Aligned_cols=35 Identities=11% Similarity=0.212 Sum_probs=29.2
Q ss_pred CcEEEEcCCHHHHHHHHHHHHHHHh--hccccccccC
Q 007603 415 DVVIQISGEYKNVQNALSEVVGRLR--HNLKSGEILN 449 (596)
Q Consensus 415 er~V~I~G~~~~V~~A~~~I~~~Lr--~~~~~~~~~~ 449 (596)
.-.|.|+|+-.+|+.|.+...+... +.++.+.+++
T Consensus 40 k~~v~v~GdvsaV~~Av~a~~~~~~~~~~~v~~~vI~ 76 (78)
T cd07054 40 KSFVVLTGDVSAVEAAVEAAEAVVGEKGLLVDSVVIP 76 (78)
T ss_pred EEEEEEEeeHHHHHHHHHHHHHHHhcCCcEEEEEEeC
Confidence 4679999999999999999988887 6677766665
No 162
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=23.87 E-value=73 Score=31.65 Aligned_cols=30 Identities=33% Similarity=0.493 Sum_probs=25.8
Q ss_pred EEEEeccCccceeecCCChHHHHHHHHhCc
Q 007603 27 FRLVCPTPVVGGLIGRSGSIISSIRRDTKC 56 (596)
Q Consensus 27 ~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga 56 (596)
++|.+....-+.|||++|.+|++|++...-
T Consensus 64 i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~ 93 (211)
T TIGR01009 64 IRVTIHTARPGIVIGKKGSEIEKLRKDLQK 93 (211)
T ss_pred eEEEEEeCCCcceeCCCchHHHHHHHHHHH
Confidence 668888888999999999999999977643
No 163
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=23.85 E-value=58 Score=32.15 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=27.7
Q ss_pred EEEEEeccCccceeecCCChHHHHHHHHhCceEEE
Q 007603 26 SFRLVCPTPVVGGLIGRSGSIISSIRRDTKCRIHC 60 (596)
Q Consensus 26 ~~rilvP~~~vg~IIGk~G~~Ik~Ir~eTga~I~V 60 (596)
.+.+-+-++..+.|||+.|+++..||--++.-++-
T Consensus 92 ~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~ 126 (208)
T COG1847 92 RVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNK 126 (208)
T ss_pred EEEEEecCCchhhhhccCCcchHHHHHHHHHHhhh
Confidence 34444566669999999999999999998876554
No 164
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=21.87 E-value=1.8e+02 Score=25.66 Aligned_cols=41 Identities=24% Similarity=0.271 Sum_probs=32.3
Q ss_pred HHhCCeEEEeCCCcccccCCCCCcEEEEcCCHHHHHHHHHHHHHHHhhcc
Q 007603 393 DVTGTDIKLVGGEQVLGCAAQNDVVIQISGEYKNVQNALSEVVGRLRHNL 442 (596)
Q Consensus 393 ~~TGa~I~I~~~~~~P~~~~~~er~V~I~G~~~~V~~A~~~I~~~Lr~~~ 442 (596)
+..++.|-+.++ -.-.+.|+|...+|+.|+..|.+.+++.|
T Consensus 61 Kaa~V~igF~DR---------FsGslvitGdvs~Ve~Al~~V~~~l~~~L 101 (111)
T PRK15468 61 KAADVHIGFLDR---------FSGALVIYGSVGAVEEALSQTVSGLGRLL 101 (111)
T ss_pred hccCcEEeeeec---------cceeEEEEccHHHHHHHHHHHHHHHHhhc
Confidence 445677777643 24678999999999999999999998743
Done!